diff --git a/bio.json.gz b/bio.json.gz
index 02e0a1d2..2a32b192 100644
--- a/bio.json.gz
+++ b/bio.json.gz
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diff --git a/bio/bash b/bio/bash
index 6d8531d2..9d7be223 160000
--- a/bio/bash
+++ b/bio/bash
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diff --git a/bio/fish b/bio/fish
index 8d492160..fd9e550b 160000
--- a/bio/fish
+++ b/bio/fish
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diff --git a/bio/json/qiime.json b/bio/json/qiime.json
index c2002643..25d20846 100644
--- a/bio/json/qiime.json
+++ b/bio/json/qiime.json
@@ -1 +1 @@
-{"name":"qiime","description":"Command line interface for QIIME 2","usage":"qiime [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"info","description":"Display information about current deployment.","usage":"qiime info [OPTIONS]","options":[{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tools","description":"Tools for working with QIIME 2 files.","usage":"qiime tools [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"cache-create","description":"Create an empty cache at the given location.","usage":"qiime tools cache-create [OPTIONS]","options":[{"names":["--cache"],"argument":"PATH","description":"Path to a nonexistent directory to be created as a cache."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cache-fetch","description":"Fetches an artifact out of a cache into a .qza.","usage":"qiime tools cache-fetch [OPTIONS]","options":[{"names":["--cache"],"argument":"DIRECTORY","description":"Path to an existing cache to load from.   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[required]"},{"names":["--input-path"],"argument":"PATH","description":"Path to file or directory that should be imported. [required]"},{"names":["--output-path"],"argument":"ARTIFACT","description":"Path where output artifact should be written. [required]"},{"names":["--input-format"],"argument":"TEXT","description":"The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type. Use `qiime tools list-formats --importable` to see which formats of input data are importable."},{"names":["--validate-level"],"argument":"[min|max]","description":"How much to validate the imported data before creating the artifact. A value of \"max\" will generally read the entire file or directory, whereas \"min\" will not usually do so. 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[required]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"export-default-theme","description":"Export the default settings.","usage":"qiime dev export-default-theme [OPTIONS]","options":[{"names":["--output-path"],"argument":"FILE","description":"Path to output the config to [required]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"import-theme","description":"Install new command line theme.","usage":"qiime dev import-theme [OPTIONS]","options":[{"names":["--theme"],"argument":"FILE","description":"Path to file containing new theme info [required]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"refresh-cache","description":"Refresh CLI cache.","usage":"qiime dev refresh-cache [OPTIONS]","options":[{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"reset-theme","description":"Reset command line theme to default.","usage":"qiime dev reset-theme [OPTIONS]","options":[{"names":["--yes"],"argument":"","description":"--help Show this message and exit."}]}]},{"name":"alignment","description":"Plugin for generating and manipulating alignments.","usage":"qiime alignment [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"mafft","description":"De novo multiple sequence alignment with MAFFT","usage":"qiime alignment mafft [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to be aligned. 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[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. 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Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"da-barplot","description":"Differential abundance bar plots","usage":"qiime composition da-barplot [OPTIONS]","options":[{"names":["--i-data"],"argument":"ARTIFACT FeatureData[DifferentialAbundance]","description":"The ANCOM-BC output to be plotted. [required]"},{"names":["--p-effect-size-label"],"argument":"TEXT","description":"Label for effect sizes in `data`. [default: 'lfc']"},{"names":["--p-feature-id-label"],"argument":"TEXT","description":"Label for feature ids in `data`. [default: 'id']"},{"names":["--p-error-label"],"argument":"TEXT","description":"Label for effect size errors in `data`."},{"names":["--p-significance-label"],"argument":"TEXT","description":"Label for statistical significance level in `data`."},{"names":["--p-significance-threshold"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Exclude features with statistical significance level greater (i.e., less significant) than this threshold."},{"names":["--p-level-delimiter"],"argument":"TEXT","description":"If feature ids encode hierarchical information, split the levels when generating feature labels in the visualization using this delimiter. [optional]"},{"names":["--p-label-limit"],"argument":"INTEGER","description":"Set the maximum length that will be viewable for axis labels. You can set this parameter if your axis labels are being cut off. [optional]"},{"names":["--p-effect-size-threshold"],"argument":"NUMBER","description":"Exclude features with an absolute value of effect size less than this threshold."},{"names":["--m-feature-ids-file"],"argument":"METADATA...","description":"Exclude features if their ids are not included in this index."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tabulate","description":"View tabular output from ANCOM-BC.","usage":"qiime composition tabulate [OPTIONS]","options":[{"names":["--i-data"],"argument":"ARTIFACT FeatureData[DifferentialAbundance]","description":"The ANCOM-BC output to be tabulated. [required]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"cutadapt","description":"Plugin for removing adapter sequences, primers, and other unwanted sequence from sequence data.","usage":"qiime cutadapt [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"demux-paired","description":"Demultiplex paired-end sequence data with barcodes in-sequence.","usage":"qiime cutadapt demux-paired [OPTIONS]","options":[{"names":["--i-seqs"],"argument":"ARTIFACT MultiplexedPairedEndBarcodeInSequence","description":"The paired-end sequences to be demultiplexed. [required]"},{"names":["--m-forward-barcodes-file"],"argument":"METADATA","description":"The sample metadata column listing the per-sample barcodes for the forward reads. [required]"},{"names":["--m-forward-barcodes-column"],"argument":"COLUMN","description":"The sample metadata column listing the per-sample barcodes for the forward reads. [required]"},{"names":["--m-reverse-barcodes-file"],"argument":"METADATA","description":"The sample metadata column listing the per-sample barcodes for the reverse reads. [optional]"},{"names":["--m-reverse-barcodes-column"],"argument":"COLUMN","description":"The sample metadata column listing the per-sample barcodes for the reverse reads. [optional]"},{"names":["--p-forward-cut"],"argument":"INTEGER","description":"Remove the specified number of bases from the forward sequences."},{"names":["--p-reverse-cut"],"argument":"INTEGER","description":"Remove the specified number of bases from the reverse sequences."},{"names":["--p-anchor-forward-barcode","--p-no-anchor-forward-barcode"],"argument":"","description":"Anchor the forward barcode. The barcode is then expected to occur in full length at the beginning (5' end) of the forward sequence. Can speed up demultiplexing if used. [default: False]"},{"names":["--p-anchor-reverse-barcode","--p-no-anchor-reverse-barcode"],"argument":"","description":"Anchor the reverse barcode. The barcode is then expected to occur in full length at the beginning (5' end) of the reverse sequence. Can speed up demultiplexing if used. [default: False]"},{"names":["--p-error-rate"],"argument":"PROPORTION","description":"The level of error tolerance, specified as the maximum allowable error rate. [default: 0.1]"},{"names":["--p-batch-size"],"argument":"INTEGER","description":"The number of samples cutadapt demultiplexes concurrently."},{"names":["--p-mixed-orientation","--p-no-mixed-orientation"],"argument":"","description":"Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file). [default: False]"},{"names":["--p-cores"],"argument":"NTHREADS","description":"Number of CPU cores to use."},{"names":["--p-minimum-length"],"argument":"INTEGER","description":"Discard reads shorter than specified value."},{"names":["--o-per-sample-sequences"],"argument":"ARTIFACT","description":"The resulting demultiplexed sequences. [required]"},{"names":["--o-untrimmed-sequences"],"argument":"ARTIFACT","description":"The sequences that were unmatched to barcodes. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"demux-single","description":"Demultiplex single-end sequence data with barcodes in-sequence.","usage":"qiime cutadapt demux-single [OPTIONS]","options":[{"names":["--i-seqs"],"argument":"ARTIFACT","description":"The single-end sequences to be demultiplexed. [required]"},{"names":["--m-barcodes-file","--m-barcodes-column"],"argument":"METADATA","description":"The sample metadata column listing the per-sample barcodes. [required]"},{"names":["--p-cut"],"argument":"INTEGER","description":"Remove the specified number of bases from the sequences. Bases are removed before demultiplexing. If a positive value is provided, bases are removed from the beginning of the sequences. If a negative value is provided, bases are removed from the end of the sequences. [default: 0]"},{"names":["--p-anchor-barcode","--p-no-anchor-barcode"],"argument":"","description":"Anchor the barcode. The barcode is then expected to occur in full length at the beginning (5' end) of the sequence. Can speed up demultiplexing if used."},{"names":["--p-error-rate"],"argument":"PROPORTION","description":"The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%)."},{"names":["--p-batch-size"],"argument":"INTEGER","description":"The number of samples cutadapt demultiplexes"},{"names":["--p-cores"],"argument":"NTHREADS","description":"Number of CPU cores to use."},{"names":["--p-minimum-length"],"argument":"INTEGER","description":"Discard reads shorter than specified value. Note,"},{"names":["--o-per-sample-sequences"],"argument":"ARTIFACT","description":"The resulting demultiplexed sequences. [required]"},{"names":["--o-untrimmed-sequences"],"argument":"ARTIFACT","description":"The sequences that were unmatched to barcodes. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"trim-paired","description":"Find and remove adapters in demultiplexed paired-end sequences.","usage":"qiime cutadapt trim-paired [OPTIONS]","options":[{"names":["--i-demultiplexed-sequences"],"argument":"ARTIFACT","description":"The paired-end sequences to be trimmed. [required]"},{"names":["--p-cores"],"argument":"NTHREADS","description":"Number of CPU cores to use."},{"names":["--p-adapter-f"],"argument":"TEXT...","description":"Sequence of an adapter ligated to the 3' end. The"},{"names":["--p-front-f"],"argument":"TEXT...","description":"Sequence of an adapter ligated to the 5' end. The"},{"names":["--p-anywhere-f"],"argument":"TEXT...","description":"Sequence of an adapter that may be ligated to the"},{"names":["--p-adapter-r"],"argument":"TEXT...","description":"Sequence of an adapter ligated to the 3' end. The"},{"names":["--p-front-r"],"argument":"TEXT...","description":"Sequence of an adapter ligated to the 5' end. The"},{"names":["--p-anywhere-r"],"argument":"TEXT...","description":"Sequence of an adapter that may be ligated to the"},{"names":["--p-error-rate"],"argument":"PROPORTION","description":"Maximum allowed error rate. [default: 0.1]"},{"names":["--p-indels","--p-no-indels"],"argument":"","description":"Allow insertions or deletions of bases when matching adapters."},{"names":["--p-times"],"argument":"INTEGER","description":"Remove multiple occurrences of an adapter if it is repeated, up to `times` times."},{"names":["--p-overlap"],"argument":"INTEGER","description":"Require at least `overlap` bases of overlap between read and adapter for an adapter to be found."},{"names":["--p-match-read-wildcards","--p-no-match-read-wildcards"],"argument":"","description":"Interpret IUPAC wildcards (e.g., N) in reads."},{"names":["--p-match-adapter-wildcards","--p-no-match-adapter-wildcards"],"argument":"","description":"Interpret IUPAC wildcards (e.g., N) in adapters."},{"names":["--p-minimum-length"],"argument":"INTEGER","description":"Discard reads shorter than specified value. Note,"},{"names":["--p-discard-untrimmed","--p-no-discard-untrimmed"],"argument":"","description":"Discard reads in which no adapter was found."},{"names":["--p-max-expected-errors"],"argument":"NUMBER","description":"Discard reads that exceed maximum expected erroneous nucleotides."},{"names":["--p-max-n"],"argument":"NUMBER","description":"Discard reads with more than COUNT N bases. If interpreted as a fraction of the read length."},{"names":["--p-quality-cutoff-5end"],"argument":"INTEGER","description":"Trim nucleotides with Phred score quality lower than threshold from 5 prime end."},{"names":["--p-quality-cutoff-3end"],"argument":"INTEGER","description":"Trim nucleotides with Phred score quality lower than threshold from 3 prime end."},{"names":["--p-quality-base"],"argument":"INTEGER","description":"How the Phred score is encoded (33 or 64)."},{"names":["--o-trimmed-sequences"],"argument":"ARTIFACT","description":"The resulting trimmed sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"trim-single","description":"Find and remove adapters in demultiplexed single-end sequences.","usage":"qiime cutadapt trim-single [OPTIONS]","options":[{"names":["--i-demultiplexed-sequences"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The single-end sequences to be trimmed. [required]"},{"names":["--p-cores"],"argument":"NTHREADS","description":"Number of CPU cores to use."},{"names":["--p-adapter"],"argument":"TEXT...","description":"Sequence of an adapter ligated to the 3' end."},{"names":["--p-front"],"argument":"TEXT...","description":"Sequence of an adapter ligated to the 5' end."},{"names":["--p-anywhere"],"argument":"TEXT...","description":"Sequence of an adapter that may be ligated to the 5' or 3' end."},{"names":["--p-error-rate"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"Maximum allowed error rate. [default: 0.1]"},{"names":["--p-indels","--p-no-indels"],"argument":"","description":"Allow insertions or deletions of bases when matching adapters."},{"names":["--p-times"],"argument":"INTEGER","description":"Remove multiple occurrences of an adapter if it is repeated, up to `times` times."},{"names":["--p-overlap"],"argument":"INTEGER","description":"Require at least `overlap` bases of overlap between read and adapter for an adapter to be found."},{"names":["--p-match-read-wildcards","--p-no-match-read-wildcards"],"argument":"","description":"Interpret IUPAC wildcards (e.g., N) in reads."},{"names":["--p-match-adapter-wildcards","--p-no-match-adapter-wildcards"],"argument":"","description":"Interpret IUPAC wildcards (e.g., N) in adapters."},{"names":["--p-minimum-length"],"argument":"INTEGER","description":"Discard reads shorter than specified value."},{"names":["--p-discard-untrimmed","--p-no-discard-untrimmed"],"argument":"","description":"Discard reads in which no adapter was found."},{"names":["--p-max-expected-errors"],"argument":"NUMBER","description":"Discard reads that exceed maximum expected erroneous nucleotides."},{"names":["--p-max-n"],"argument":"NUMBER","description":"Discard reads with more than COUNT N bases."},{"names":["--p-quality-cutoff-5end"],"argument":"INTEGER","description":"Trim nucleotides with Phred score quality lower than threshold from 5 prime end."},{"names":["--p-quality-cutoff-3end"],"argument":"INTEGER","description":"Trim nucleotides with Phred score quality lower than threshold from 3 prime end."},{"names":["--p-quality-base"],"argument":"INTEGER","description":"How the Phred score is encoded (33 or 64)."},{"names":["--o-trimmed-sequences"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The resulting trimmed sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"dada2","description":"Plugin for sequence quality control with DADA2.","usage":"qiime dada2 [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"denoise-ccs","description":"Denoise and dereplicate single-end Pacbio CCS","usage":"qiime dada2 denoise-ccs [OPTIONS]","options":[{"names":["--i-demultiplexed-seqs"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The single-end demultiplexed PacBio CCS sequences to be denoised. [required]"},{"names":["--p-front"],"argument":"TEXT","description":"Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded. Each read is re-oriented if the reverse complement of the read is a better match to the provided primer sequence. This is recommended for PacBio CCS reads, which come in a random mix of forward and reverse-complement orientations. [required]"},{"names":["--p-adapter"],"argument":"TEXT","description":"Sequence of an adapter ligated to the 3' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded. [required]"},{"names":["--p-max-mismatch"],"argument":"INTEGER","description":"The number of mismatches to tolerate when matching reads to primer sequences - see http://benjjneb.github.io/dada2/ for complete details. [default: 2]"},{"names":["--p-indels","--p-no-indels"],"argument":"","description":"Allow insertions or deletions of bases when matching adapters. Note that primer matching can be significantly slower, currently about 4x slower"},{"names":["--p-trunc-len"],"argument":"INTEGER","description":"Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed. Note: Since Pacbio CCS sequences were normally with very high quality scores, there is no need to truncate the Pacbio CCS sequences."},{"names":["--p-trim-left"],"argument":"INTEGER","description":"Position at which sequences should be trimmed due to low quality. This trims the 5' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]"},{"names":["--p-max-ee"],"argument":"NUMBER","description":"Reads with number of expected errors higher than this value will be discarded. [default: 2.0]"},{"names":["--p-trunc-q"],"argument":"INTEGER","description":"Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]"},{"names":["--p-min-len"],"argument":"INTEGER","description":"Remove reads with length less than minLen. minLen is enforced after trimming and truncation. For 16S Pacbio CCS, suggest 1000. [default: 20]"},{"names":["--p-max-len"],"argument":"INTEGER","description":"Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length. For 16S Pacbio CCS, suggest 1600. [default: 0]"},{"names":["--p-pooling-method"],"argument":"TEXT Choices('independent', 'pseudo')","description":"The method used to pool samples for denoising. \"independent\": Samples are denoised indpendently. \"pseudo\": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs."},{"names":["--p-chimera-method"],"argument":"TEXT Choices('consensus', 'none', 'pooled')","description":"The method used to remove chimeras. \"none\": No chimera removal is performed. \"pooled\": All reads are pooled prior to chimera detection. \"consensus\": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: 'consensus']"},{"names":["--p-min-fold-parent-over-abundance"],"argument":"NUMBER","description":"The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). Suggest 3.5. This parameter has no effect if chimera-method is \"none\"."},{"names":["--p-allow-one-off","--p-no-allow-one-off"],"argument":"","description":"Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is True. If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera. [default: False]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]"},{"names":["--p-n-reads-learn"],"argument":"INTEGER","description":"The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model."},{"names":["--p-hashed-feature-ids","--p-no-hashed-feature-ids"],"argument":"","description":"If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]"},{"names":["--p-retain-all-samples","--p-no-retain-all-samples"],"argument":"","description":"If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table."},{"names":["--o-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting feature table. [required]"},{"names":["--o-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]"},{"names":["--o-denoising-stats"],"argument":"ARTIFACT SampleData[DADA2Stats]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"denoise-paired","description":"Denoise and dereplicate paired-end sequences","usage":"qiime dada2 denoise-paired [OPTIONS]","options":[{"names":["--i-demultiplexed-seqs"],"argument":"ARTIFACT SampleData[PairedEndSequencesWithQuality]","description":"The paired-end demultiplexed sequences to be denoised. [required]"},{"names":["--p-trunc-len-f"],"argument":"INTEGER","description":"Position at which forward read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]"},{"names":["--p-trunc-len-r"],"argument":"INTEGER","description":"Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]"},{"names":["--p-trim-left-f"],"argument":"INTEGER","description":"Position at which forward read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]"},{"names":["--p-trim-left-r"],"argument":"INTEGER","description":"Position at which reverse read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]"},{"names":["--p-max-ee-f"],"argument":"NUMBER","description":"Forward reads with number of expected errors higher than this value will be discarded. [default: 2.0]"},{"names":["--p-max-ee-r"],"argument":"NUMBER","description":"Reverse reads with number of expected errors higher than this value will be discarded. [default: 2.0]"},{"names":["--p-trunc-q"],"argument":"INTEGER","description":"Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len-f` or `trunc-len-r` (depending on the direction of the read) it is discarded. [default: 2]"},{"names":["--p-min-overlap"],"argument":"INTEGER","description":"The minimum length of the overlap required for merging the forward and reverse reads."},{"names":["--p-pooling-method"],"argument":"TEXT Choices('independent', 'pseudo')","description":"The method used to pool samples for denoising. \"independent\": Samples are denoised indpendently. \"pseudo\": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs."},{"names":["--p-chimera-method"],"argument":"TEXT Choices('consensus', 'none', 'pooled')","description":"The method used to remove chimeras. \"none\": No chimera removal is performed. \"pooled\": All reads are pooled prior to chimera detection. \"consensus\": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: 'consensus']"},{"names":["--p-min-fold-parent-over-abundance"],"argument":"NUMBER","description":"The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is \"none\". [default: 1.0]"},{"names":["--p-allow-one-off","--p-no-allow-one-off"],"argument":"","description":"Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is TrueIf True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera."},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]"},{"names":["--p-n-reads-learn"],"argument":"INTEGER","description":"The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model."},{"names":["--p-hashed-feature-ids","--p-no-hashed-feature-ids"],"argument":"","description":"If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]"},{"names":["--p-retain-all-samples","--p-no-retain-all-samples"],"argument":"","description":"If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table."},{"names":["--o-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting feature table. [required]"},{"names":["--o-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence, and these sequences will be the joined paired-end sequences. [required]"},{"names":["--o-denoising-stats"],"argument":"ARTIFACT SampleData[DADA2Stats]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"denoise-pyro","description":"Denoise and dereplicate single-end pyrosequences","usage":"qiime dada2 denoise-pyro [OPTIONS]","options":[{"names":["--i-demultiplexed-seqs"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The single-end demultiplexed pyrosequencing sequences (e.g. 454, IonTorrent) to be denoised."},{"names":["--p-trunc-len"],"argument":"INTEGER","description":"Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed [required]"},{"names":["--p-trim-left"],"argument":"INTEGER","description":"Position at which sequences should be trimmed due to low quality. This trims the 5' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]"},{"names":["--p-max-ee"],"argument":"NUMBER","description":"Reads with number of expected errors higher than this value will be discarded. [default: 2.0]"},{"names":["--p-trunc-q"],"argument":"INTEGER","description":"Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]"},{"names":["--p-max-len"],"argument":"INTEGER","description":"Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length. [default: 0]"},{"names":["--p-pooling-method"],"argument":"TEXT Choices('independent', 'pseudo')","description":"The method used to pool samples for denoising. \"independent\": Samples are denoised independently. \"pseudo\": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs."},{"names":["--p-chimera-method"],"argument":"TEXT Choices('consensus', 'none', 'pooled')","description":"The method used to remove chimeras. \"none\": No chimera removal is performed. \"pooled\": All reads are pooled prior to chimera detection. \"consensus\": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: 'consensus']"},{"names":["--p-min-fold-parent-over-abundance"],"argument":"NUMBER","description":"The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is \"none\". [default: 1.0]"},{"names":["--p-allow-one-off","--p-no-allow-one-off"],"argument":"","description":"Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is True. If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera. [default: False]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]"},{"names":["--p-n-reads-learn"],"argument":"INTEGER","description":"The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model."},{"names":["--p-hashed-feature-ids","--p-no-hashed-feature-ids"],"argument":"","description":"If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]"},{"names":["--p-retain-all-samples","--p-no-retain-all-samples"],"argument":"","description":"If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table."},{"names":["--o-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting feature table. [required]"},{"names":["--o-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]"},{"names":["--o-denoising-stats"],"argument":"ARTIFACT SampleData[DADA2Stats]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"denoise-single","description":"Denoise and dereplicate single-end sequences","usage":"qiime dada2 denoise-single [OPTIONS]","options":[{"names":["--p-trunc-len"],"argument":"INTEGER","description":"Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed [required]"},{"names":["--p-trim-left"],"argument":"INTEGER","description":"Position at which sequences should be trimmed due to low quality. This trims the 5' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]"},{"names":["--p-max-ee"],"argument":"NUMBER","description":"Reads with number of expected errors higher than this value will be discarded. [default: 2.0]"},{"names":["--p-trunc-q"],"argument":"INTEGER","description":"Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]"},{"names":["--p-pooling-method"],"argument":"TEXT Choices('independent', 'pseudo')","description":"The method used to pool samples for denoising. \"independent\": Samples are denoised independently. \"pseudo\": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs."},{"names":["--p-chimera-method"],"argument":"TEXT Choices('consensus', 'none', 'pooled')","description":"The method used to remove chimeras. \"none\": No chimera removal is performed. \"pooled\": All reads are pooled prior to chimera detection. \"consensus\": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: 'consensus']"},{"names":["--p-min-fold-parent-over-abundance"],"argument":"NUMBER","description":"The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. 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Smaller numbers will result in a shorter run time but a less reliable error model."},{"names":["--p-hashed-feature-ids","--p-no-hashed-feature-ids"],"argument":"","description":"If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]"},{"names":["--p-retain-all-samples","--p-no-retain-all-samples"],"argument":"","description":"If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table."},{"names":["--o-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting feature table. [required]"},{"names":["--o-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]"},{"names":["--o-denoising-stats"],"argument":"ARTIFACT SampleData[DADA2Stats]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"deblur","description":"Plugin for sequence quality control with Deblur.","usage":"qiime deblur [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"denoise-16S","description":"Deblur sequences using a 16S positive filter.","usage":"qiime deblur denoise-16S [OPTIONS]","options":[{"names":["--p-trim-length"],"argument":"INTEGER","description":"Sequence trim length, specify -1 to disable trimming. [required]"},{"names":["--p-sample-stats","--p-no-sample-stats"],"argument":"","description":"If true, gather stats per sample. [default: False]"},{"names":["--p-mean-error"],"argument":"NUMBER","description":"The mean per nucleotide error, used for original sequence estimate. [default: 0.005]"},{"names":["--p-indel-prob"],"argument":"NUMBER","description":"Insertion/deletion (indel) probability (same for N indels). [default: 0.01]"},{"names":["--p-indel-max"],"argument":"INTEGER","description":"Maximum number of insertion/deletions. [default: 3]"},{"names":["--p-min-reads"],"argument":"INTEGER","description":"Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]"},{"names":["--p-min-size"],"argument":"INTEGER","description":"In each sample, discard all features with an abundance less than min-size. [default: 2]"},{"names":["--p-jobs-to-start"],"argument":"NTHREADS","description":"Number of jobs to start (if to run in parallel)."},{"names":["--p-hashed-feature-ids","--p-no-hashed-feature-ids"],"argument":"","description":"If true, hash the feature IDs. [default: True]"},{"names":["--p-left-trim-len"],"argument":"INTEGER","description":"Sequence trimming from the 5' end. A value of 0 will"},{"names":["--o-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting denoised feature table. [required]"},{"names":["--o-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting feature sequences. [required]"},{"names":["--o-stats"],"argument":"ARTIFACT","description":"Per-sample stats if requested."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"denoise-other","description":"Deblur sequences using a user-specified positive filter.","usage":"qiime deblur denoise-other [OPTIONS]","options":[{"names":["--i-demultiplexed-seqs"],"argument":"","description":"ARTIFACT SampleData[SequencesWithQuality |"},{"names":["--i-reference-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Positive filtering database. Keep all sequences aligning to these sequences. [required]"},{"names":["--p-trim-length"],"argument":"INTEGER","description":"Sequence trim length, specify -1 to disable trimming. [required]"},{"names":["--p-sample-stats","--p-no-sample-stats"],"argument":"","description":"If true, gather stats per sample. [default: False]"},{"names":["--p-mean-error"],"argument":"NUMBER","description":"The mean per nucleotide error, used for original sequence estimate. [default: 0.005]"},{"names":["--p-indel-prob"],"argument":"NUMBER","description":"Insertion/deletion (indel) probability (same for N indels). [default: 0.01]"},{"names":["--p-indel-max"],"argument":"INTEGER","description":"Maximum number of insertion/deletions. [default: 3]"},{"names":["--p-min-reads"],"argument":"INTEGER","description":"Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]"},{"names":["--p-min-size"],"argument":"INTEGER","description":"In each sample, discard all features with an abundance less than min-size. [default: 2]"},{"names":["--p-jobs-to-start"],"argument":"NTHREADS","description":"Number of jobs to start (if to run in parallel)."},{"names":["--p-hashed-feature-ids","--p-no-hashed-feature-ids"],"argument":"","description":"If true, hash the feature IDs. [default: True]"},{"names":["--p-left-trim-len"],"argument":"INTEGER","description":"Sequence trimming from the 5' end. A value of 0 will"},{"names":["--o-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting denoised feature table. [required]"},{"names":["--o-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting feature sequences. [required]"},{"names":["--o-stats"],"argument":"ARTIFACT","description":"Per-sample stats if requested. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"visualize-stats","description":"Visualize Deblur stats per sample.","usage":"qiime deblur visualize-stats [OPTIONS]","options":[{"names":["--i-deblur-stats"],"argument":"ARTIFACT","description":"DeblurStats Summary statistics of the Deblur process. [required]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"demux","description":"Plugin for demultiplexing & viewing sequence quality.","usage":"qiime demux [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"emp-paired","description":"Demultiplex paired-end sequence data generated with the EMP protocol.","usage":"qiime demux emp-paired [OPTIONS]","options":[{"names":["--i-seqs"],"argument":"ARTIFACT EMPPairedEndSequences","description":"The paired-end sequences to be demultiplexed."},{"names":["--m-barcodes-file","--m-barcodes-column"],"argument":"METADATA","description":"The sample metadata column containing the per-sample barcodes. [required]"},{"names":["--p-golay-error-correction","--p-no-golay-error-correction"],"argument":"","description":"Perform 12nt Golay error correction on the barcode reads. [default: True]"},{"names":["--p-rev-comp-barcodes","--p-no-rev-comp-barcodes"],"argument":"","description":"If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing."},{"names":["--p-rev-comp-mapping-barcodes","--p-no-rev-comp-mapping-barcodes"],"argument":"","description":"If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]"},{"names":["--p-ignore-description-mismatch","--p-no-ignore-description-mismatch"],"argument":"","description":"If enabled, ignore mismatches in sequence record description fields. [default: False]"},{"names":["--o-error-correction-details"],"argument":"ARTIFACT ErrorCorrectionDetails","description":"Detail about the barcode error corrections. [required]"},{"names":["--o-per-sample-sequences"],"argument":"ARTIFACT","description":"SampleData[PairedEndSequencesWithQuality]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"emp-single","description":"Demultiplex sequence data generated with the EMP protocol.","usage":"qiime demux emp-single [OPTIONS]","options":[{"names":["--m-barcodes-file","--m-barcodes-column"],"argument":"METADATA","description":"The sample metadata column containing the per-sample barcodes. [required]"},{"names":["--p-golay-error-correction","--p-no-golay-error-correction"],"argument":"","description":"Perform 12nt Golay error correction on the barcode reads. [default: True]"},{"names":["--p-rev-comp-barcodes","--p-no-rev-comp-barcodes"],"argument":"","description":"If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing."},{"names":["--p-rev-comp-mapping-barcodes","--p-no-rev-comp-mapping-barcodes"],"argument":"","description":"If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]"},{"names":["--p-ignore-description-mismatch","--p-no-ignore-description-mismatch"],"argument":"","description":"If enabled, ignore mismatches in sequence record description fields. [default: False]"},{"names":["--o-per-sample-sequences"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The resulting demultiplexed sequences. [required]"},{"names":["--o-error-correction-details"],"argument":"ARTIFACT ErrorCorrectionDetails","description":"Detail about the barcode error corrections. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-samples","description":"Filter samples out of demultiplexed data.","usage":"qiime demux filter-samples [OPTIONS]","options":[{"names":["--i-demux"],"argument":"ARTIFACT","description":"The demultiplexed data from which samples should be filtered. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata indicating which sample ids to filter. [required]"},{"names":["--p-where"],"argument":"TEXT","description":"Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partition-samples-paired","description":"Split demultiplexed sequence data into partitions.","usage":"qiime demux partition-samples-paired [OPTIONS]","options":[{"names":["--i-demux"],"argument":"ARTIFACT SampleData[PairedEndSequencesWithQuality]","description":"The demultiplexed sequences to partition. [required]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the demultiplexed"},{"names":["--o-partitioned-demux"],"argument":"ARTIFACTS...","description":"Collection[SampleData[PairedEndSequencesWithQuality]]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partition-samples-single","description":"Split demultiplexed sequence data into partitions.","usage":"qiime demux partition-samples-single [OPTIONS]","options":[{"names":["--i-demux"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The demultiplexed sequences to partition. [required]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the demultiplexed"},{"names":["--o-partitioned-demux"],"argument":"ARTIFACTS...","description":"Collection[SampleData[SequencesWithQuality]]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"subsample-paired","description":"Subsample paired-end sequences without replacement.","usage":"qiime demux subsample-paired [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT SampleData[PairedEndSequencesWithQuality]","description":"The demultiplexed sequences to be subsampled."},{"names":["--p-fraction"],"argument":"PROPORTION Range(0, 1, inclusive_start=False)","description":"The fraction of sequences to retain in subsample."},{"names":["--o-subsampled-sequences"],"argument":"ARTIFACT","description":"SampleData[PairedEndSequencesWithQuality]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"subsample-single","description":"Subsample single-end sequences without replacement.","usage":"qiime demux subsample-single [OPTIONS]","options":[{"names":["--p-fraction"],"argument":"PROPORTION Range(0, 1, inclusive_start=False)","description":"The fraction of sequences to retain in subsample."},{"names":["--o-subsampled-sequences"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The subsampled sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"summarize","description":"Summarize counts per sample.","usage":"qiime demux summarize [OPTIONS]","options":[{"names":["--p-n"],"argument":"INTEGER","description":"The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tabulate-read-counts","description":"Tabulate counts per sample","usage":"qiime demux tabulate-read-counts [OPTIONS]","options":[{"names":["--o-counts"],"argument":"ARTIFACT","description":"ImmutableMetadata [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"diversity","description":"Plugin for exploring community diversity.","usage":"qiime diversity [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"adonis","description":"adonis PERMANOVA test for beta group significance","usage":"qiime diversity adonis [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata containing formula terms. [required]"},{"names":["--p-formula"],"argument":"TEXT","description":"Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula \"treatment+block\" would test whether the input distance matrix partitions based on \"treatment\" and \"block\" sample metadata. The formula \"treatment*block\" would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of parallel processes to run"},{"names":["--p-permutations"],"argument":"INTEGER","description":"The number of permutations to be run when computing"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"alpha","description":"Alpha diversity","usage":"qiime diversity alpha [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The feature table containing the samples for which"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence","description":"The feature table containing the samples for which"},{"names":["--o-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample alpha diversities."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"alpha-correlation","description":"Alpha diversity correlation","usage":"qiime diversity alpha-correlation [OPTIONS]","options":[{"names":["--i-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of alpha diversity values by sample. [required]"},{"names":["--p-method"],"argument":"TEXT Choices('spearman', 'pearson')","description":"The correlation test to be applied."},{"names":["--p-intersect-ids","--p-no-intersect-ids"],"argument":"","description":"If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs. [default: False]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"alpha-group-significance","description":"Alpha diversity comparisons","usage":"qiime diversity alpha-group-significance [OPTIONS]","options":[{"names":["--i-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of alpha diversity values by sample. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata. [required]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"alpha-phylogenetic","description":"Alpha diversity (phylogenetic)","usage":"qiime diversity alpha-phylogenetic [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]","description":"The feature table containing the samples for which alpha diversity should be computed. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"The alpha diversity metric to be computed. [required]"},{"names":["--o-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample alpha diversities. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"alpha-rarefaction","description":"Alpha rarefaction curves","usage":"qiime diversity alpha-rarefaction [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table to compute rarefaction curves from. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Optional phylogeny for phylogenetic metrics."},{"names":["--p-max-depth"],"argument":"INTEGER","description":"The maximum rarefaction depth. Must be greater than min-depth. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata."},{"names":["--p-min-depth"],"argument":"INTEGER","description":"The minimum rarefaction depth."},{"names":["--p-steps"],"argument":"INTEGER","description":"The number of rarefaction depths to include between min-depth and max-depth. [default: 10]"},{"names":["--p-iterations"],"argument":"INTEGER","description":"The number of rarefied feature tables to compute at each step. [default: 10]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta","description":"Beta diversity","usage":"qiime diversity beta [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]","description":"The feature table containing the samples over which beta diversity should be computed. [required]"},{"names":["--p-metric"],"argument":"{aitchison, braycurtis, canberra, canberra_adkins, chebyshev, cityblock, correlation, cosine, dice, euclidean, hamming, jaccard, jensenshannon, kulsinski, matching, minkowski, rogerstanimoto, russellrao, seuclidean, sokalmichener, sokalsneath, sqeuclidean, yule}","description":"The beta diversity metric to be computed."},{"names":["--p-pseudocount"],"argument":"INTEGER","description":"A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = 'auto', one job will be launched for each identified CPU core on the host. [default: 1]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix The resulting distance matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-correlation","description":"Beta diversity correlation","usage":"qiime diversity beta-correlation [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Numeric metadata column from which to compute pairwise Euclidean distances [required]"},{"names":["--p-method"],"argument":"TEXT Choices('spearman', 'pearson')","description":"The correlation test to be applied in the Mantel test. [default: 'spearman']"},{"names":["--p-permutations"],"argument":"INTEGER","description":"The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]"},{"names":["--p-intersect-ids","--p-no-intersect-ids"],"argument":"","description":"If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]"},{"names":["--p-label1"],"argument":"TEXT","description":"Label for `distance-matrix` in the output visualization. [default: 'Distance Matrix']"},{"names":["--p-label2"],"argument":"TEXT","description":"Label for `metadata-distance-matrix` in the output visualization. [default: 'Metadata']"},{"names":["--p-permutations"],"argument":"INTEGER","description":"The number of permutations to be run when computing p-values."},{"names":["--o-metadata-distance-matrix"],"argument":"ARTIFACT","description":"The Distance Matrix produced from the metadata column and used in the mantel test [required]"},{"names":["--o-mantel-scatter-visualization"],"argument":"VISUALIZATION","description":"Scatter plot rendering of the manteltest results [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-group-significance","description":"Beta diversity group significance","usage":"qiime diversity beta-group-significance [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples."},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Categorical sample metadata column. [required]"},{"names":["--p-method"],"argument":"TEXT Choices('permanova', 'anosim', 'permdisp')","description":"The group significance test to be applied."},{"names":["--p-pairwise","--p-no-pairwise"],"argument":"","description":"Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column. [default: False]"},{"names":["--p-permutations"],"argument":"INTEGER","description":"The number of permutations to be run when computing p-values. [default: 999]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-phylogenetic","description":"Beta diversity (phylogenetic)","usage":"qiime diversity beta-phylogenetic [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]","description":"The feature table containing the samples over which beta diversity should be computed. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]"},{"names":["--p-metric"],"argument":"{generalized_unifrac, unweighted_unifrac, weighted_normalized_unifrac, weighted_unifrac}","description":"The beta diversity metric to be computed. [required]"},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."},{"names":["--p-variance-adjusted","--p-no-variance-adjusted"],"argument":"","description":"Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]"},{"names":["--p-alpha"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized. [optional]"},{"names":["--p-bypass-tips","--p-no-bypass-tips"],"argument":"","description":"In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"The resulting distance matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-rarefaction","description":"Beta diversity rarefaction","usage":"qiime diversity beta-rarefaction [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table upon which to perform beta diversity rarefaction analyses. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required for phylogenetic metrics] [optional]"},{"names":["--p-metric"],"argument":"{aitchison, braycurtis, canberra, canberra_adkins, chebyshev, cityblock, correlation, cosine, dice, euclidean, generalized_unifrac, hamming, jaccard, jensenshannon, kulsinski, matching, minkowski, rogerstanimoto, russellrao, seuclidean, sokalmichener, sokalsneath, sqeuclidean, unweighted_unifrac, weighted_normalized_unifrac, weighted_unifrac, yule}","description":"The beta diversity metric to be computed. [required]"},{"names":["--p-clustering-method"],"argument":"{nj, upgma}","description":"Samples can be clustered with neighbor joining or UPGMA. An arbitrary rarefaction trial will be used for the tree, and the remaining trials are used to calculate the support of the internal nodes of that tree. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata used for the Emperor jackknifed PCoA plot. [required]"},{"names":["--p-sampling-depth"],"argument":"INTEGER","description":"The total frequency that each sample should be rarefied to prior to computing the diversity metric. [required]"},{"names":["--p-iterations"],"argument":"INTEGER","description":"Number of times to rarefy the feature table at a given sampling depth. [default: 10]"},{"names":["--p-clustering-method"],"argument":"TEXT Choices('nj', 'upgma')","description":"Samples can be clustered with neighbor joining or UPGMA. An arbitrary rarefaction trial will be used for the tree, and the remaining trials are used to calculate the support of the internal nodes of that tree. [required]"},{"names":["--p-correlation-method"],"argument":"TEXT Choices('pearson', 'spearman')","description":"The Mantel correlation test to be applied when computing correlation between beta diversity distance matrices. [default: 'spearman']"},{"names":["--p-color-scheme"],"argument":"{BrBG, BrBG_r, PRGn, PRGn_r, PiYG, PiYG_r, PuOr, PuOr_r, RdBu, RdBu_r, RdGy, RdGy_r, RdYlBu, RdYlBu_r, RdYlGn, RdYlGn_r}","description":"The matplotlib color scheme to generate the heatmap with."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"bioenv","description":"bioenv","usage":"qiime diversity bioenv [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples."},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"core-metrics","description":"Core diversity metrics (non-phylogenetic)","usage":"qiime diversity core-metrics [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table containing the samples over which diversity metrics should be computed. [required]"},{"names":["--p-sampling-depth"],"argument":"INTEGER","description":"The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata to use in the emperor plots. [required]"},{"names":["--p-with-replacement","--p-no-with-replacement"],"argument":"","description":"Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"[beta methods only] - The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = 'auto', one job will be launched for each identified CPU core on the host. [default: 1]"},{"names":["--p-ignore-missing-samples","--p-no-ignore-missing-samples"],"argument":"","description":"If set to `True` samples and features without metadata are included by setting all metadata values to: \"This element has no metadata\". By default an exception will be raised if missing elements are encountered. Note, this flag only takes effect if there is at least one overlapping element."},{"names":["--o-rarefied-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting rarefied feature table. [required]"},{"names":["--o-observed-features-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Observed Features values by sample. [required]"},{"names":["--o-shannon-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Shannon diversity values by sample. [required]"},{"names":["--o-evenness-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Pielou's evenness values by sample. [required]"},{"names":["--o-jaccard-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of Jaccard distances between pairs of samples. [required]"},{"names":["--o-bray-curtis-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of Bray-Curtis distances between pairs of samples. [required]"},{"names":["--o-jaccard-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from Jaccard distances between samples. [required]"},{"names":["--o-bray-curtis-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from Bray-Curtis distances Bray-Curtis. [required]"},{"names":["--o-jaccard-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from Jaccard. [required]"},{"names":["--o-bray-curtis-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from Bray-Curtis. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"core-metrics-phylogenetic","description":"Core diversity metrics (phylogenetic and non-phylogenetic)","usage":"qiime diversity core-metrics-phylogenetic [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table containing the samples over which diversity metrics should be computed. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]"},{"names":["--p-sampling-depth"],"argument":"INTEGER","description":"The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata to use in the emperor plots. [required]"},{"names":["--p-with-replacement","--p-no-with-replacement"],"argument":"","description":"Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]"},{"names":["--o-rarefied-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting rarefied feature table. [required]"},{"names":["--o-faith-pd-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Faith PD values by sample. [required]"},{"names":["--o-observed-features-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Observed Features values by sample. [required]"},{"names":["--o-shannon-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Shannon diversity values by sample. [required]"},{"names":["--o-evenness-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Pielou's evenness values by sample. [required]"},{"names":["--o-unweighted-unifrac-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of unweighted UniFrac distances between pairs of samples. [required]"},{"names":["--o-weighted-unifrac-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of weighted UniFrac distances between pairs of samples. [required]"},{"names":["--o-jaccard-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of Jaccard distances between pairs of samples. [required]"},{"names":["--o-bray-curtis-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of Bray-Curtis distances between pairs of samples. [required]"},{"names":["--o-unweighted-unifrac-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from unweighted UniFrac distances between samples. [required]"},{"names":["--o-weighted-unifrac-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from weighted UniFrac distances between samples. [required]"},{"names":["--o-jaccard-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from Jaccard distances between samples. [required]"},{"names":["--o-bray-curtis-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from Bray-Curtis distances samples. [required]"},{"names":["--o-unweighted-unifrac-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from unweighted UniFrac. [required]"},{"names":["--o-weighted-unifrac-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from weighted UniFrac. [required]"},{"names":["--o-jaccard-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from Jaccard. [required]"},{"names":["--o-bray-curtis-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from Bray-Curtis. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-alpha-diversity","description":"Filter samples from an alpha diversity metric.","usage":"qiime diversity filter-alpha-diversity [OPTIONS]","options":[{"names":["--i-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Alpha diversity sample data to filter by sample. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata used to select samples to retain from the sample data (default) or select samples to exclude using the `exclude-ids` parameter. [required]"},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered alpha diversity artifact. If not provided, all samples in `metadata` that are also in the input alpha diversity artifact will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"If `True`, the samples selected by `metadata` or the `where` parameters will be excluded from the filtered alpha diversity artifact instead of being retained."},{"names":["--o-filtered-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-distance-matrix","description":"Filter samples from a distance matrix.","usage":"qiime diversity filter-distance-matrix [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix to filter by sample. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude-ids` when selecting samples to discard. [required]"},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained."},{"names":["--o-filtered-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix filtered to include samples matching"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"mantel","description":"Apply the Mantel test to two distance matrices","usage":"qiime diversity mantel [OPTIONS]","options":[{"names":["--i-dm1"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--i-dm2"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--p-method"],"argument":"{spearman, pearson}","description":"The correlation test to be applied in the Mantel test."},{"names":["--p-permutations"],"argument":"INTEGER","description":"The number of permutations to be run when computing p-values."},{"names":["--p-intersect-ids","--p-no-intersect-ids"],"argument":"","description":"If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]"},{"names":["--p-label1"],"argument":"TEXT","description":"Label for `dm1` in the output visualization."},{"names":["--p-label2"],"argument":"TEXT","description":"Label for `dm2` in the output visualization."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partial-procrustes","description":"Partial Procrustes","usage":"qiime diversity partial-procrustes [OPTIONS]","options":[{"names":["--i-reference"],"argument":"ARTIFACT","description":"The ordination matrix to which data is fitted to. [required]"},{"names":["--i-other"],"argument":"ARTIFACT","description":"The ordination matrix that's fitted to the reference ordination. [required]"},{"names":["--m-pairing-file"],"argument":"METADATA","description":"The metadata file."},{"names":["--m-pairing-column"],"argument":"COLUMN","description":"The metadata column describing sample pairs which exist. [required]"},{"names":["--p-dimensions"],"argument":"INTEGER","description":"The number of dimensions to use when fitting the two matrices of the reference ordination. [required]"},{"names":["--o-transformed"],"argument":"ARTIFACT","description":"The 'other' ordination transformed into the space of the reference ordination. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"pcoa","description":"Principal Coordinate Analysis","usage":"qiime diversity pcoa [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"The distance matrix on which PCoA should be computed. [required]"},{"names":["--p-number-of-dimensions"],"argument":"INTEGER","description":"Dimensions to reduce the distance matrix to. This number determines how many eigenvectors and eigenvalues are returned,and influences the choice of algorithm used to compute them. By default, uses the default eigendecomposition method, SciPy's eigh, which computes all eigenvectors and eigenvalues in an exact manner. For very large matrices, this is expected to be slow. If a value is specified for this parameter, then the fast, heuristic eigendecomposition algorithm fsvd is used, which only computes and returns the number of dimensions specified, but suffers some degree of accuracy loss, the magnitude of which varies across different datasets. [optional]"},{"names":["--o-pcoa"],"argument":"ARTIFACT","description":"The resulting PCoA matrix."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"pcoa-biplot","description":"Principal Coordinate Analysis Biplot","usage":"qiime diversity pcoa-biplot [OPTIONS]","options":[{"names":["--i-pcoa"],"argument":"ARTIFACT","description":"The PCoA where the features will be projected onto."},{"names":["--i-features"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Variables to project onto the PCoA matrix [required]"},{"names":["--o-biplot"],"argument":"ARTIFACT","description":"The resulting PCoA matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"procrustes-analysis","description":"Procrustes Analysis","usage":"qiime diversity procrustes-analysis [OPTIONS]","options":[{"names":["--i-reference"],"argument":"ARTIFACT","description":"The ordination matrix to which data is fitted to. [required]"},{"names":["--i-other"],"argument":"ARTIFACT","description":"The ordination matrix that's fitted to the reference ordination. [required]"},{"names":["--p-dimensions"],"argument":"INTEGER","description":"The number of dimensions to use when fitting the two matrices [default: 5]"},{"names":["--p-permutations"],"argument":"VALUE","description":"The number of permutations to be run when computing p-values. Supplying a value of `disable` will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]"},{"names":["--o-transformed-reference"],"argument":"ARTIFACT","description":"A normalized version of the \"reference\" ordination matrix. [required]"},{"names":["--o-transformed-other"],"argument":"ARTIFACT","description":"A normalized and fitted version of the \"other\" ordination matrix. [required]"},{"names":["--o-disparity-results"],"argument":"ARTIFACT","description":"The sum of the squares of the pointwise differences between the two input datasets & its p value. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tsne","description":"t-distributed stochastic neighbor embedding","usage":"qiime diversity tsne [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"The distance matrix on which t-SNE should be computed. [required]"},{"names":["--p-number-of-dimensions"],"argument":"INTEGER","description":"Dimensions to reduce the distance matrix to. [required]"},{"names":["--p-perplexity"],"argument":"NUMBER","description":"Provide the balance between local and global structure. Low values concentrate on local structure. [default: 25.0]"},{"names":["--p-n-iter"],"argument":"INTEGER","description":"[default: 1000]"},{"names":["--p-learning-rate"],"argument":"NUMBER","description":"Controls how much the weights are adjusted at each update. [default: 200.0]"},{"names":["--p-early-exaggeration"],"argument":"NUMBER","description":"Affects the tightness of the shown clusters. Larger values increase the distance between natural clusters in the embedded space. [default: 12.0]"},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--o-tsne"],"argument":"ARTIFACT","description":"The resulting t-SNE matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"umap","description":"Uniform Manifold Approximation and Projection","usage":"qiime diversity umap [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"The distance matrix on which UMAP should be computed. [required]"},{"names":["--p-number-of-dimensions"],"argument":"INTEGER","description":"Dimensions to reduce the distance matrix to."},{"names":["--p-n-neighbors"],"argument":"INTEGER","description":"Provide the balance between local and global structure."},{"names":["--p-min-dist"],"argument":"NUMBER","description":"Controls the cluster size. Low values cause clumpier clusters."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--o-umap"],"argument":"ARTIFACT","description":"The resulting UMAP matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"diversity-lib","description":"Plugin for computing community diversity.","usage":"qiime diversity-lib [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"alpha-passthrough","description":"Alpha Passthrough (non-phylogenetic)","usage":"qiime diversity-lib alpha-passthrough [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table containing the samples for which a selected metric should be computed. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"The alpha diversity metric to be computed. [required]"},{"names":["--o-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample values for the chosen metric. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-passthrough","description":"Beta Passthrough (non-phylogenetic)","usage":"qiime diversity-lib beta-passthrough [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table containing the samples over which beta diversity should be computed. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"The beta diversity metric to be computed. [required]"},{"names":["--p-pseudocount"],"argument":"INTEGER","description":"A pseudocount to handle zeros for compositional metrics."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = 'auto', one job will be launched for each identified CPU core on the host. [default: 1]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix The resulting distance matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-phylogenetic-passthrough","description":"Beta Phylogenetic Passthrough","usage":"qiime diversity-lib beta-phylogenetic-passthrough [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table containing the samples over which beta diversity should be computed. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"The beta diversity metric to be computed. [required]"},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."},{"names":["--p-variance-adjusted","--p-no-variance-adjusted"],"argument":"","description":"Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]"},{"names":["--p-alpha"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized. [optional]"},{"names":["--p-bypass-tips","--p-no-bypass-tips"],"argument":"","description":"In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix The resulting distance matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"bray-curtis","description":"Bray-Curtis Dissimilarity","usage":"qiime diversity-lib bray-curtis [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency]","description":"The feature table containing the samples for which Bray-Curtis dissimilarity should be computed."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = 'auto', one job will be launched for each identified CPU core on the host. [default: 1]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix for Bray-Curtis dissimilarity"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."},{"names":["--o-distance-matrix"],"argument":"bray-curtis-dm.qza","description":"# ### example: use 'auto' to run on all of host system's available CPU cores"}]},{"name":"faith-pd","description":"Faith's Phylogenetic Diversity","usage":"qiime diversity-lib faith-pd [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The feature table containing the samples for which"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence","description":"The feature table containing the samples for which"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that   Phylogeny[Rooted] correspond to the feature identifiers in the table."},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."},{"names":["--o-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample values for Faith's Phylogenetic Diversity. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"jaccard","description":"Jaccard Distance","usage":"qiime diversity-lib jaccard [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The feature table containing the samples for which"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence","description":"The feature table containing the samples for which"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = 'auto', one job will be launched for each identified CPU core on the host. [default: 1]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix for Jaccard index [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."},{"names":["--o-distance-matrix"],"argument":"jaccard-dm.qza","description":"# ### example: use 'auto' to run on all of host system's available CPU cores"}]},{"name":"observed-features","description":"Observed Features","usage":"qiime diversity-lib observed-features [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The feature table containing the samples for which the"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence","description":"The feature table containing the samples for which the"},{"names":["--o-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample counts of observed features. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"pielou-evenness","description":"Pielou's Evenness","usage":"qiime diversity-lib pielou-evenness [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency]","description":"The feature table containing the samples for which Pielou's evenness should be computed. [required]"},{"names":["--p-drop-undefined-samples","--p-no-drop-undefined-samples"],"argument":"","description":"Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector. [default: False]"},{"names":["--o-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample values for Pielou's Evenness. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"shannon-entropy","description":"Shannon's Entropy","usage":"qiime diversity-lib shannon-entropy [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency]","description":"The feature table containing the samples for which Shannon's Entropy should be computed. [required]"},{"names":["--p-drop-undefined-samples","--p-no-drop-undefined-samples"],"argument":"","description":"Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector. [default: False]"},{"names":["--o-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample values for Shannon's Entropy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"unweighted-unifrac","description":"Unweighted Unifrac","usage":"qiime diversity-lib unweighted-unifrac [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The feature table containing the samples for which"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence","description":"The feature table containing the samples for which"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that   Phylogeny[Rooted] correspond to the feature identifiers in the table."},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."},{"names":["--p-bypass-tips","--p-no-bypass-tips"],"argument":"","description":"In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix for Unweighted Unifrac. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."},{"names":["--o-distance-matrix"],"argument":"unweighted-unifrac-dm.qza","description":"# ### example: to run on n cores, replace 1 here with your preferred integer"}]},{"name":"weighted-unifrac","description":"Weighted Unifrac","usage":"qiime diversity-lib weighted-unifrac [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency]","description":"The feature table containing the samples for which Weighted Unifrac should be computed. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that"},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."},{"names":["--p-bypass-tips","--p-no-bypass-tips"],"argument":"","description":"In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix for Unweighted Unifrac. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."},{"names":["--o-distance-matrix"],"argument":"weighted-unifrac-dm.qza","description":"# ### example: to run on n cores, replace 1 here with your preferred integer"}]}]},{"name":"emperor","description":"Plugin for ordination plotting with Emperor.","usage":"qiime emperor [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"biplot","description":"Visualize and Interact with Principal Coordinates Analysis","usage":"qiime emperor biplot [OPTIONS]","options":[{"names":["--i-biplot"],"argument":"ARTIFACT","description":"The principal coordinates matrix to be plotted. [required]"},{"names":["--m-sample-metadata-file"],"argument":"METADATA...","description":"The sample metadata [required]"},{"names":["--m-feature-metadata-file"],"argument":"METADATA...","description":"The feature metadata (useful to manipulate the arrows in the plot)."},{"names":["--p-ignore-missing-samples","--p-no-ignore-missing-samples"],"argument":"","description":"This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \"This sample has no metadata\". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]"},{"names":["--p-invert","--p-no-invert"],"argument":"","description":"If specified, the point and arrow coordinates will be swapped. [default: False]"},{"names":["--p-number-of-features"],"argument":"","description":"INTEGER"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"plot","description":"Visualize and Interact with Principal Coordinates Analysis","usage":"qiime emperor plot [OPTIONS]","options":[{"names":["--i-pcoa"],"argument":"ARTIFACT","description":"The principal coordinates matrix to be plotted. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata. [required]"},{"names":["--p-ignore-missing-samples","--p-no-ignore-missing-samples"],"argument":"","description":"This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \"This sample has no metadata\". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]"},{"names":["--p-ignore-pcoa-features","--p-no-ignore-pcoa-features"],"argument":"","description":"Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the `biplot` method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised. [default: False]"},{"names":["--p-custom-axes"],"argument":"TEXT...","description":"Numeric sample metadata columns that should be included as axes in the Emperor plot."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"procrustes-plot","description":"Visualize and Interact with a procrustes plot","usage":"qiime emperor procrustes-plot [OPTIONS]","options":[{"names":["--i-reference-pcoa"],"argument":"ARTIFACT","description":"The reference ordination matrix to be plotted. [required]"},{"names":["--i-other-pcoa"],"argument":"ARTIFACT","description":"The \"other\" ordination matrix to be plotted (the one that was fitted to the reference). [required]"},{"names":["--i-m2-stats"],"argument":"ARTIFACT ProcrustesStatistics","description":"The M^2 value of the procrustes analysis & its associated p value. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata. [required]"},{"names":["--p-custom-axes"],"argument":"TEXT...","description":"Numeric sample metadata columns that should be included as axes in the Emperor plot."},{"names":["--p-ignore-missing-samples","--p-no-ignore-missing-samples"],"argument":"","description":"This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \"This sample has no metadata\". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"feature-classifier","description":"Plugin for taxonomic classification.","usage":"qiime feature-classifier [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"blast","description":"BLAST+ local alignment search.","usage":"qiime feature-classifier blast [OPTIONS]","options":[{"names":["--i-query"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query sequences. [required]"},{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences. Incompatible with blastdb."},{"names":["--i-blastdb"],"argument":"ARTIFACT","description":"BLAST indexed database. Incompatible with"},{"names":["--p-maxaccepts"],"argument":"INTEGER","description":"Maximum number of hits to keep for each query."},{"names":["--p-perc-identity"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if percent identity to query is lower."},{"names":["--p-query-cov"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. [default: 0.8]"},{"names":["--p-strand"],"argument":"TEXT Choices('both', 'plus', 'minus')","description":"Align against reference sequences in forward (\"plus\"), reverse (\"minus\"), or both directions (\"both\"). [default: 'both']"},{"names":["--p-evalue"],"argument":"NUMBER","description":"BLAST expectation value (E) threshold for saving hits. [default: 0.001]"},{"names":["--p-output-no-hits","--p-no-output-no-hits"],"argument":"","description":"Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. Set to FALSE to mirror default BLAST search."},{"names":["--p-num-threads"],"argument":"NTHREADS","description":"Number of threads (CPUs) to use in the BLAST search. Pass 0 to use all available CPUs."},{"names":["--o-search-results"],"argument":"ARTIFACT","description":"FeatureData[BLAST6] Top hits for each query. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-consensus-blast","description":"BLAST+ consensus taxonomy classifier","usage":"qiime feature-classifier classify-consensus-blast [OPTIONS]","options":[{"names":["--i-query"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query sequences. [required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"reference taxonomy labels. [required]"},{"names":["--i-blastdb"],"argument":"ARTIFACT","description":"BLAST indexed database. Incompatible with"},{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences. Incompatible with blastdb."},{"names":["--p-maxaccepts"],"argument":"INTEGER","description":"Maximum number of hits to keep for each query."},{"names":["--p-perc-identity"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if percent identity to query is lower."},{"names":["--p-query-cov"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. [default: 0.8]"},{"names":["--p-strand"],"argument":"TEXT Choices('both', 'plus', 'minus')","description":"Align against reference sequences in forward (\"plus\"), reverse (\"minus\"), or both directions (\"both\"). [default: 'both']"},{"names":["--p-evalue"],"argument":"NUMBER","description":"BLAST expectation value (E) threshold for saving hits. [default: 0.001]"},{"names":["--p-output-no-hits","--p-no-output-no-hits"],"argument":"","description":"Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. Set to FALSE to mirror default BLAST search."},{"names":["--p-min-consensus"],"argument":"NUMBER","description":"Minimum fraction of assignments must match top hit to be accepted as consensus assignment."},{"names":["--p-unassignable-label"],"argument":"TEXT","description":"Annotation given to sequences without any hits."},{"names":["--p-num-threads"],"argument":"NTHREADS","description":"Number of threads (CPUs) to use in the BLAST search. Pass 0 to use all available CPUs."},{"names":["--o-classification"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomy classifications of query sequences."},{"names":["--o-search-results"],"argument":"ARTIFACT","description":"FeatureData[BLAST6] Top hits for each query. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-consensus-vsearch","description":"VSEARCH-based consensus taxonomy classifier","usage":"qiime feature-classifier classify-consensus-vsearch [OPTIONS]","options":[{"names":["--i-query"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query Sequences. [required]"},{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences. [required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Reference taxonomy labels. [required]"},{"names":["--p-maxaccepts"],"argument":"VALUE","description":"Maximum number of hits to keep for each query."},{"names":["--p-perc-identity"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if percent identity to query is lower."},{"names":["--p-query-cov"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8]"},{"names":["--p-strand"],"argument":"TEXT Choices('both', 'plus')","description":"Align against reference sequences in forward (\"plus\") or both directions (\"both\")."},{"names":["--p-search-exact","--p-no-search-exact"],"argument":"","description":"Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity, query-cov, maxaccepts, and maxrejects settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False]"},{"names":["--p-top-hits-only","--p-no-top-hits-only"],"argument":"","description":"Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False]"},{"names":["--p-maxhits"],"argument":"VALUE","description":"Maximum number of hits to show once the search is terminated."},{"names":["--p-maxrejects"],"argument":"VALUE","description":"Maximum number of non-matching target sequences to consider before stopping the search."},{"names":["--p-output-no-hits","--p-no-output-no-hits"],"argument":"","description":"Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs."},{"names":["--p-weak-id"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0]"},{"names":["--p-threads"],"argument":"NTHREADS","description":"Number of threads to use for job parallelization. Pass 0 to use one per available CPU. [default: 1]"},{"names":["--p-min-consensus"],"argument":"NUMBER","description":"Minimum fraction of assignments must match top hit to be accepted as consensus assignment."},{"names":["--p-unassignable-label"],"argument":"TEXT","description":"Annotation given to sequences without any hits."},{"names":["--o-classification"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomy classifications of query sequences. [required]"},{"names":["--o-search-results"],"argument":"ARTIFACT","description":"FeatureData[BLAST6] Top hits for each query. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-hybrid-vsearch-sklearn","description":"ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier","usage":"qiime feature-classifier classify-hybrid-vsearch-sklearn","options":[{"names":["--i-query"],"argument":"ARTIFACT","description":"Query Sequences. [required]"},{"names":["--i-reference-reads"],"argument":"ARTIFACT","description":"Reference sequences. [required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT","description":"Reference taxonomy labels. [required]"},{"names":["--i-classifier"],"argument":"ARTIFACT","description":"Pre-trained sklearn taxonomic classifier for classifying the reads. [required]"},{"names":["--p-maxaccepts"],"argument":"VALUE","description":"Maximum number of hits to keep for each query. Set to \"all\" to keep all hits > perc-identity similarity. Note that if strand=both, maxaccepts will keep N hits for each direction (if searches in the opposite direction yield results that exceed the minimum perc-identity). In those cases use maxhits to control the total number of hits returned. This option works in pair with maxrejects. The search process sorts target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if the first target sequence passes the acceptation criteria, it is accepted as best hit and the search process stops for that query. If maxaccepts is set to a higher value, more hits are accepted. If maxaccepts and maxrejects are both set to \"all\", the complete database is searched. [default: 10]"},{"names":["--p-perc-identity"],"argument":"PROPORTION","description":"Percent sequence similarity to use for PREFILTER. Reject match if percent identity to query is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.5]"},{"names":["--p-query-cov"],"argument":"PROPORTION","description":"Query coverage threshold to use for PREFILTER. Reject match if query alignment coverage per high-scoring pair is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.8]"},{"names":["--p-strand"],"argument":"{'both', 'plus'}","description":"Align against reference sequences in forward (\"plus\") or both directions (\"both\"). [default: 'both']"},{"names":["--p-min-consensus"],"argument":"NUMBER","description":"Minimum fraction of assignments must match top hit to be accepted as consensus assignment."},{"names":["--p-maxhits"],"argument":"VALUE","description":"max hits [default: 'all']"},{"names":["--p-maxrejects"],"argument":"VALUE","description":"max rejects [default: 'all']"},{"names":["--p-reads-per-batch"],"argument":"VALUE","description":"Number of reads to process in each batch for sklearn classification. If \"auto\", this parameter is autoscaled to min(number of query sequences / threads, 20000). [default: 'auto']"},{"names":["--p-confidence"],"argument":"VALUE Float","description":"Confidence threshold for limiting taxonomic depth. Set to \"disable\" to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments."},{"names":["--p-read-orientation"],"argument":"{'same', 'reverse-complement', 'auto'}","description":"Direction of reads with respect to reference sequences in pre-trained sklearn classifier. same will cause reads to be classified unchanged; reverse-complement will cause reads to be reversed and complemented prior to classification. \"auto\" will autodetect orientation based on the confidence estimates for the first 100 reads. [default: 'auto']"},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of threads to use for job parallelization. [default: 1]"},{"names":["--p-prefilter","--p-no-prefilter"],"argument":"","description":"Toggle positive filter of query sequences on or off. [default: True]"},{"names":["--p-sample-size"],"argument":"INTEGER","description":"Randomly extract the given number of sequences from the reference database to use for prefiltering. This parameter is ignored if `prefilter` is disabled. [default: 1000]"},{"names":["--p-randseed"],"argument":"INTEGER","description":"Use integer as a seed for the pseudo-random"},{"names":["--o-classification"],"argument":"ARTIFACT","description":"Taxonomy classifications of query sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-sklearn","description":"Pre-fitted sklearn-based taxonomy classifier","usage":"qiime feature-classifier classify-sklearn [OPTIONS]","options":[{"names":["--i-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The feature data to be classified. [required]"},{"names":["--i-classifier"],"argument":"ARTIFACT","description":"TaxonomicClassifier The taxonomic classifier for classifying the reads."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]"},{"names":["--p-pre-dispatch"],"argument":"TEXT","description":"\"all\" or expression, as in \"3*n_jobs\". The number of batches (of tasks) to be pre-dispatched."},{"names":["--p-read-orientation"],"argument":"TEXT Choices('same', 'reverse-complement', 'auto')","description":"Direction of reads with respect to reference sequences. same will cause reads to be classified unchanged; reverse-complement will cause reads to be reversed and complemented prior to classification. \"auto\" will autodetect orientation based on the confidence estimates for the first 100 reads."},{"names":["--o-classification"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"extract-reads","description":"Extract reads from reference sequences.","usage":"qiime feature-classifier extract-reads [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"[required]"},{"names":["--p-f-primer"],"argument":"TEXT","description":"forward primer sequence (5' -> 3'). [required]"},{"names":["--p-r-primer"],"argument":"TEXT","description":"reverse primer sequence (5' -> 3'). Do not use reverse-complemented primer sequence. [required]"},{"names":["--p-trim-right"],"argument":"INTEGER","description":"trim-right nucleotides are removed from the 3' end if trim-right is positive. Applied before trunc-len and trim-left. [default: 0]"},{"names":["--p-trunc-len"],"argument":"INTEGER","description":"read is cut to trunc-len if trunc-len is positive. Applied after trim-right but before trim-left."},{"names":["--p-trim-left"],"argument":"INTEGER","description":"trim-left nucleotides are removed from the 5' end if trim-left is positive. Applied after trim-right and trunc-len. [default: 0]"},{"names":["--p-identity"],"argument":"NUMBER","description":"minimum combined primer match identity threshold."},{"names":["--p-min-length"],"argument":"INTEGER","description":"Minimum amplicon length. Shorter amplicons are"},{"names":["--p-max-length"],"argument":"INTEGER","description":"Maximum amplicon length. Longer amplicons are"},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of seperate processes to run."},{"names":["--p-read-orientation"],"argument":"TEXT Choices('both', 'forward', 'reverse')","description":"Orientation of primers relative to the sequences: \"forward\" searches for primer hits in the forward direction, \"reverse\" searches reverse-complement, and \"both\" searches both directions."},{"names":["--o-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"find-consensus-annotation","description":"Find consensus among multiple annotations.","usage":"qiime feature-classifier find-consensus-annotation [OPTIONS]","options":[{"names":["--i-search-results"],"argument":"ARTIFACT FeatureData[BLAST6]","description":"Search results in BLAST6 output format [required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"reference taxonomy labels. [required]"},{"names":["--p-unassignable-label"],"argument":"TEXT","description":"Annotation given when no consensus is found."},{"names":["--o-consensus-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Consensus taxonomy and scores. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fit-classifier-naive-bayes","description":"Train the naive_bayes classifier","usage":"qiime feature-classifier fit-classifier-naive-bayes \n    [OPTIONS]","options":[{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"[required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--i-class-weight"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"[optional]"},{"names":["--p-classify--alpha"],"argument":"NUMBER","description":"[default: 0.001]"},{"names":["--p-classify--chunk-size"],"argument":"INTEGER","description":"[default: 20000]"},{"names":["--p-classify--fit-prior","--p-no-classify--fit-prior"],"argument":"","description":"[default: False]"},{"names":["--p-feat-ext--alternate-sign","--p-no-feat-ext--alternate-sign"],"argument":"","description":"[default: False]"},{"names":["--p-feat-ext--binary","--p-no-feat-ext--binary"],"argument":"","description":"[default: False]"},{"names":["--p-verbose","--p-no-verbose"],"argument":"","description":"[default: False]"},{"names":["--p-classify--class-prior"],"argument":"TEXT","description":"[default: 'null']"},{"names":["--p-feat-ext--analyzer"],"argument":"TEXT","description":"[default: 'char_wb']"},{"names":["--p-feat-ext--preprocessor"],"argument":"TEXT","description":"[default: 'null']"},{"names":["--p-feat-ext--stop-words"],"argument":"TEXT","description":"[default: 'null']"},{"names":["--p-feat-ext--strip-accents"],"argument":"TEXT","description":"[default: 'null']"},{"names":["--p-feat-ext--tokenizer"],"argument":"TEXT","description":"[default: 'null']"},{"names":["--p-feat-ext--decode-error"],"argument":"TEXT","description":"[default: 'strict']"},{"names":["--p-feat-ext--encoding"],"argument":"TEXT","description":"[default: 'utf-8']"},{"names":["--p-feat-ext--input"],"argument":"TEXT","description":"[default: 'content']"},{"names":["--p-feat-ext--lowercase","--p-no-feat-ext--lowercase"],"argument":"","description":"[default: True]"},{"names":["--p-feat-ext--n-features"],"argument":"INTEGER","description":"[default: 8192]"},{"names":["--p-feat-ext--ngram-range"],"argument":"TEXT","description":"[default: '[7, 7]']"},{"names":["--p-feat-ext--norm"],"argument":"TEXT","description":"[default: 'l2']"},{"names":["--p-feat-ext--token-pattern"],"argument":"TEXT","description":"[default: '(?u)\\\\b\\\\w\\\\w+\\\\b']"},{"names":["--o-classifier"],"argument":"ARTIFACT TaxonomicClassifier","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fit-classifier-sklearn","description":"Train an almost arbitrary scikit-learn classifier","usage":"qiime feature-classifier fit-classifier-sklearn [OPTIONS]","options":[{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"[required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--i-class-weight"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"[optional]"},{"names":["--p-classifier-specification"],"argument":"TEXT","description":"[required]"},{"names":["--o-classifier"],"argument":"ARTIFACT TaxonomicClassifier","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"makeblastdb","description":"Make BLAST database.","usage":"qiime feature-classifier makeblastdb [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Input reference sequences. [required]"},{"names":["--o-database"],"argument":"ARTIFACT","description":"Output BLAST database."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"vsearch-global","description":"VSEARCH global alignment search","usage":"qiime feature-classifier vsearch-global [OPTIONS]","options":[{"names":["--i-query"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query Sequences. [required]"},{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences. [required]"},{"names":["--p-perc-identity"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if percent identity to query is lower."},{"names":["--p-query-cov"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8]"},{"names":["--p-strand"],"argument":"TEXT Choices('both', 'plus')","description":"Align against reference sequences in forward (\"plus\") or both directions (\"both\")."},{"names":["--p-search-exact","--p-no-search-exact"],"argument":"","description":"Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity, query-cov, maxaccepts, and maxrejects settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False]"},{"names":["--p-top-hits-only","--p-no-top-hits-only"],"argument":"","description":"Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False]"},{"names":["--p-output-no-hits","--p-no-output-no-hits"],"argument":"","description":"Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs."},{"names":["--p-weak-id"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0]"},{"names":["--p-threads"],"argument":"NTHREADS","description":"Number of threads to use for job parallelization. Pass 0 to use one per available CPU. [default: 1]"},{"names":["--o-search-results"],"argument":"ARTIFACT","description":"FeatureData[BLAST6] Top hits for each query. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"feature-table","description":"Plugin for working with sample by feature tables.","usage":"qiime feature-table [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"core-features","description":"Identify core features in table","usage":"qiime feature-table core-features [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to use in core features calculations. [required]"},{"names":["--p-min-fraction"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 0.5]"},{"names":["--p-max-fraction"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 1.0]"},{"names":["--p-steps"],"argument":"INTEGER","description":"The number of steps to take between `min-fraction` and"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-features","description":"Filter features from table","usage":"qiime feature-table filter-features [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table from which features should be filtered. [required]"},{"names":["--p-min-frequency"],"argument":"INTEGER","description":"The minimum total frequency that a feature must have to be retained. [default: 0]"},{"names":["--p-max-frequency"],"argument":"INTEGER","description":"The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]"},{"names":["--p-min-samples"],"argument":"INTEGER","description":"The minimum number of samples that a feature must be observed in to be retained. [default: 0]"},{"names":["--p-max-samples"],"argument":"INTEGER","description":"The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied). [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Feature metadata used with `where` parameter when selecting features to retain, or with `exclude-ids` when selecting features to discard."},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the feature table will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"If true, the features selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. [default: False]"},{"names":["--p-filter-empty-samples","--p-no-filter-empty-samples"],"argument":"","description":"If true, drop any samples where none of the retained features are present. [default: True]"},{"names":["--p-allow-empty-table","--p-no-allow-empty-table"],"argument":"","description":"If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]"},{"names":["--o-filtered-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting feature table filtered by feature. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-features-conditionally","description":"Filter features from a table based on abundance and prevalence","usage":"qiime feature-table filter-features-conditionally [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"The feature table from which features should be filtered. [required]"},{"names":["--p-abundance"],"argument":"PROPORTION","description":"The minimum relative abundance for a feature to be retained. [required]"},{"names":["--p-prevalence"],"argument":"PROPORTION","description":"The minimum portion of samples that a feature must have a relative abundance of at least `abundance` to be retained. [required]"},{"names":["--p-allow-empty-table","--p-no-allow-empty-table"],"argument":"","description":"If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]"},{"names":["--o-filtered-table"],"argument":"ARTIFACT","description":"The resulting feature table filtered by feature. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-samples","description":"Filter samples from table","usage":"qiime feature-table filter-samples [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"The feature table from which samples should be filtered. [required]"},{"names":["--p-min-frequency"],"argument":"INTEGER","description":"The minimum total frequency that a sample must have to be retained. [default: 0]"},{"names":["--p-max-frequency"],"argument":"INTEGER","description":"The maximum total frequency that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]"},{"names":["--p-min-features"],"argument":"INTEGER","description":"The minimum number of features that a sample must have to be retained. [default: 0]"},{"names":["--p-max-features"],"argument":"INTEGER","description":"The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied). [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude-ids` when selecting samples to discard."},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"If true, the samples selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. [default: False]"},{"names":["--p-filter-empty-features","--p-no-filter-empty-features"],"argument":"","description":"If true, features which are not present in any retained samples are dropped. [default: True]"},{"names":["--p-allow-empty-table","--p-no-allow-empty-table"],"argument":"","description":"If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]"},{"names":["--o-filtered-table"],"argument":"ARTIFACT","description":"The resulting feature table filtered by sample. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-seqs","description":"Filter features from sequences","usage":"qiime feature-table filter-seqs [OPTIONS]","options":[{"names":["--i-data"],"argument":"ARTIFACT FeatureData[Sequence¹ | AlignedSequence²]","description":"The sequences from which features should be filtered. [required]"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Table containing feature ids used for id-based filtering. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Feature metadata used for id-based filtering, with `where` parameter when selecting features to retain, or with `exclude-ids` when selecting features to discard."},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained. [default: False]"},{"names":["--o-filtered-data"],"argument":"ARTIFACT FeatureData[Sequence¹ | AlignedSequence²]","description":"The resulting filtered sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"group","description":"Group samples or features by a metadata column","usage":"qiime feature-table group [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The table to group samples or features on. [required]"},{"names":["--p-axis"],"argument":"TEXT Choices('feature', 'sample')","description":"Along which axis to group. Each ID in the given axis must exist in `metadata`. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"A column defining the groups. Each unique value will become a new ID for the table on the given `axis`."},{"names":["--p-mode"],"argument":"TEXT Choices('mean-ceiling', 'median-ceiling', 'sum')","description":"How to combine samples or features within a group. `sum` will sum the frequencies across all samples or features within a group; `mean-ceiling` will take the ceiling of the mean of these frequencies; `median-ceiling` will take the ceiling of the median of these frequencies. [required]"},{"names":["--o-grouped-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"A table that has been grouped along the given `axis`. IDs on that axis are replaced by values in the `metadata` column. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"heatmap","description":"Generate a heatmap representation of a feature table","usage":"qiime feature-table heatmap [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to visualize. [required]"},{"names":["--m-sample-metadata-file"],"argument":"","description":"METADATA"},{"names":["--m-sample-metadata-column"],"argument":"COLUMN  MetadataColumn[Categorical]","description":"Annotate the sample IDs with these sample metadata values. When metadata is present and `cluster`='feature', samples will be sorted by the metadata values. [optional]"},{"names":["--m-feature-metadata-file"],"argument":"","description":"METADATA"},{"names":["--m-feature-metadata-column"],"argument":"COLUMN  MetadataColumn[Categorical]","description":"Annotate the feature IDs with these feature metadata values. When metadata is present and `cluster`='sample', features will be sorted by the metadata values. [optional]"},{"names":["--p-normalize","--p-no-normalize"],"argument":"","description":"Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table."},{"names":["--p-title"],"argument":"TEXT","description":"Optional custom plot title. [optional]"},{"names":["--p-cluster"],"argument":"TEXT Choices('both', 'features', 'none', 'samples')","description":"Specify which axes to cluster. [default: 'both']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"merge","description":"Combine multiple tables","usage":"qiime feature-table merge [OPTIONS]","options":[{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. 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Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"presence-absence","description":"Convert to presence/absence","usage":"qiime feature-table presence-absence [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency]","description":"The feature table to be converted into presence/absence abundances. [required]"},{"names":["--o-presence-absence-table"],"argument":"ARTIFACT FeatureTable[PresenceAbsence]","description":"The resulting presence/absence feature table."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"rarefy","description":"Rarefy table","usage":"qiime feature-table rarefy [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to be rarefied. 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Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"relative-frequency","description":"Convert to relative frequencies","usage":"qiime feature-table relative-frequency [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to be converted into relative frequencies. 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[required]"},{"names":["--p-subsampling-depth"],"argument":"","description":"INTEGER"},{"names":["--p-axis"],"argument":"TEXT Choices('sample', 'feature')","description":"The axis to sample over. If \"sample\" then samples will be randomly selected to be retained. If \"feature\" then a random set of features will be selected to be retained. [required]"},{"names":["--o-sampled-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting subsampled feature table. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"summarize","description":"Summarize table","usage":"qiime feature-table summarize [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | PresenceAbsence]","description":"The feature table to be summarized. 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[required]"},{"names":["--o-summary"],"argument":"VISUALIZATION","description":"Visual summary of feature table [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. 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[required]"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | PresenceAbsence |   RelativeFrequency","description":"The input feature table. [required]"},{"names":["--o-sample-frequencies"],"argument":"ARTIFACT","description":"ImmutableMetadata Observed feature count and total frequencies per"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tabulate-seqs","description":"View sequence associated with each feature","usage":"qiime feature-table tabulate-seqs [OPTIONS]","options":[{"names":["--i-data"],"argument":"ARTIFACT FeatureData[Sequence | AlignedSequence]","description":"The feature sequences to be tabulated. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACTS... Collection[FeatureData[Taxonomy]]","description":"The taxonomic classifications of the tabulated features. [optional]"},{"names":["--p-merge-method"],"argument":"TEXT Choices('strict', 'union', 'intersect')","description":"Method that joins data sets [default: 'strict']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Any additional metadata for the tabulated features."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"transpose","description":"Transpose a feature table.","usage":"qiime feature-table transpose [OPTIONS]","options":[{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"fragment-insertion","description":"Plugin for extending phylogenies.","usage":"qiime fragment-insertion [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"classify-otus-experimental","description":"Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.","usage":"qiime fragment-insertion classify-otus-experimental [OPTIONS]","options":[{"names":["--i-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences used for a 'sepp' run to produce the 'tree'. 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Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-features","description":"Filter fragments in tree from table.","usage":"qiime fragment-insertion filter-features [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"A feature-table which needs to filtered down to those fragments that are contained in the tree, e.g. result of a Deblur or DADA2 run. [required]"},{"names":["--i-tree"],"argument":"ARTIFACT","description":"The tree resulting from inserting fragments into a"},{"names":["--o-filtered-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The input table minus those fragments that were not part of the tree. 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Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"sepp","description":"Insert fragment sequences using SEPP into reference phylogenies.","usage":"qiime fragment-insertion sepp [OPTIONS]","options":[{"names":["--i-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to insert into the reference tree."},{"names":["--i-reference-database"],"argument":"ARTIFACT SeppReferenceDatabase","description":"The reference database to insert the representative sequences into. [required]"},{"names":["--p-alignment-subset-size"],"argument":"INTEGER","description":"Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. [default: 1000]"},{"names":["--p-placement-subset-size"],"argument":"INTEGER","description":"The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. Further reading: https://github.com/smirarab/sepp/blob/master/tutorial/ sepp-tutorial.md#sample-datasets-default-parameters."},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of threads to use. Pass 0 to use one per available core. [default: 1]"},{"names":["--p-debug","--p-no-debug"],"argument":"","description":"Collect additional run information to STDOUT for debugging. Temporary directories will not be removed if run fails. 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[required]"},{"names":["--p-formula"],"argument":"TEXT","description":"R-style formula specifying the model. All terms must be present in the sample metadata or metadata-transformable artifacts and can be continuous or categorical metadata columns. Formulae will be in the format \"a ~ b + c\", where \"a\" is the metric (dependent variable) and \"b\" and \"c\" are independent covariates. Use \"+\" to add a variable; \"+ a:b\" to add an interaction between variables a and b; \"*\" to include a variable and all interactions; and \"-\" to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [required]"},{"names":["--p-sstype"],"argument":"TEXT Choices('I', 'II', 'III')","description":"Type of sum of squares calculation to perform (I, II, or III). [default: 'II']"},{"names":["--p-repeated-measures","--p-no-repeated-measures"],"argument":"","description":"Perform ANOVA as a repeated measures ANOVA. Implemented via statsmodels, which has the following limitations: Currently, only fully balanced within-subject designs are supported. Calculation of between-subject effects and corrections for violation of sphericity are not yet implemented. [default: False]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"The column containing individual ID with repeated measures to account for.This should not be included in the formula. [optional]"},{"names":["--p-rm-aggregate","--p-no-rm-aggregate"],"argument":"","description":"If the data set contains more than a single observation per individual id and cell of the specified model, this function will be used to aggregate the data by the mean before running the ANOVA. Only applicable for repeated measures ANOVA. [default: False]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"feature-volatility","description":"Feature volatility analysis","usage":"qiime longitudinal feature-volatility [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata containing collection time (state) values for each sample. Must contain exclusively numeric values. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [optional]"},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation. 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[required]"},{"names":["--o-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Regressor]","description":"Trained sample regressor. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"first-differences","description":"Compute first differences or difference from","usage":"qiime longitudinal first-differences [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table to optionally use for computing first differences. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (time) variable information. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"Numerical metadata or artifact column to test."},{"names":["--p-replicate-handling"],"argument":"TEXT Choices('error', 'random', 'drop')","description":"Choose how replicate samples are handled. If replicates are detected, \"error\" causes method to fail; \"drop\" will discard all replicated samples; \"random\" chooses one representative at random from among replicates. [default: 'error']"},{"names":["--p-baseline"],"argument":"NUMBER","description":"A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static differences instead of first differences (which are calculated if no value is given for baseline). If a \"baseline\" value is provided, sample differences at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]"},{"names":["--o-first-differences"],"argument":"ARTIFACT SampleData[FirstDifferences]","description":"Series of first differences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"first-distances","description":"Compute first distances or distance from baseline","usage":"qiime longitudinal first-distances [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (time) variable information. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [required]"},{"names":["--p-baseline"],"argument":"NUMBER","description":"A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a \"baseline\" value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column."},{"names":["--p-replicate-handling"],"argument":"TEXT Choices('error', 'random', 'drop')","description":"Choose how replicate samples are handled. If replicates are detected, \"error\" causes method to fail; \"drop\" will discard all replicated samples; \"random\" chooses one representative at random from among replicates. [default: 'error']"},{"names":["--o-first-distances"],"argument":"ARTIFACT SampleData[FirstDifferences]","description":"Series of first distances. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"linear-mixed-effects","description":"Linear mixed effects modeling","usage":"qiime longitudinal linear-mixed-effects [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table containing metric. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (time) variable information. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"Dependent variable column name. Must be a column name located in the metadata or feature table files."},{"names":["--p-group-columns"],"argument":"TEXT","description":"Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine mean structure of \"metric\". [optional]"},{"names":["--p-random-effects"],"argument":"TEXT","description":"Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine the variance and covariance structure (random effects) of \"metric\". To add a random slope, the same value passed to \"state-column\" should be passed here. A random intercept for each individual is set by default and does not need to be passed here. [optional]"},{"names":["--p-palette"],"argument":"TEXT","description":"Color palette to use for generating boxplots."},{"names":["--p-lowess","--p-no-lowess"],"argument":"","description":"Estimate locally weighted scatterplot smoothing. Note that this will eliminate confidence interval plotting. [default: False]"},{"names":["--p-ci"],"argument":"NUMBER","description":"Size of the confidence interval for the regression"},{"names":["--p-formula"],"argument":"TEXT","description":"R-style formula to use for model specification. A formula must be used if the \"metric\" parameter is None. Note that the metric and group columns specified in the formula will override metric and group columns that are passed separately as parameters to this method. Formulae will be in the format \"a ~ b + c\", where \"a\" is the metric (dependent variable) and \"b\" and \"c\" are independent covariates. Use \"+\" to add a variable; \"+ a:b\" to add an interaction between variables a and b; \"*\" to include a variable and all interactions; and \"-\" to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [optional]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"maturity-index","description":"Microbial maturity index prediction.","usage":"qiime longitudinal maturity-index [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"metadata file(s) [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Numeric metadata column containing sampling time (state) data to use as prediction target. [required]"},{"names":["--p-group-by"],"argument":"TEXT","description":"Categorical metadata column to use for plotting and significance testing between main treatment groups. [required]"},{"names":["--p-control"],"argument":"TEXT","description":"Value of group-by to use as control group. The regression model will be trained using only control group data, and the maturity scores of other groups consequently will be assessed relative to this group. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Optional metadata column containing IDs for individual subjects. Adds individual subject (spaghetti) vectors to volatility charts if a column name is provided. [optional]"},{"names":["--p-estimator"],"argument":"{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor[DecisionTree], AdaBoostRegressor[ExtraTrees], ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}","description":"Regression model to use for prediction."},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-test-size"],"argument":"PROPORTION","description":"Fraction of input samples to exclude from training set and use for classifier testing."},{"names":["--p-step"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"If optimize-feature-selection is True, step is the percentage of features to remove at each iteration."},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-optimize-feature-selection","--p-no-optimize-feature-selection"],"argument":"","description":"Automatically optimize input feature selection using recursive feature elimination."},{"names":["--p-stratify","--p-no-stratify"],"argument":"","description":"Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: False]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--p-feature-count"],"argument":"INTEGER","description":"Filter feature table to include top N most important features."},{"names":["--o-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Regressor]","description":"Trained sample estimator. [required]"},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy. [required]"},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[RegressorPredictions]","description":"Predicted target values for each input sample. [required]"},{"names":["--o-model-summary"],"argument":"VISUALIZATION","description":"Summarized parameter and (if enabled) feature selection information for the trained estimator. [required]"},{"names":["--o-accuracy-results"],"argument":"VISUALIZATION","description":"Accuracy results visualization. [required]"},{"names":["--o-maz-scores"],"argument":"ARTIFACT SampleData[RegressorPredictions]","description":"Microbiota-for-age z-score predictions. [required]"},{"names":["--o-clustermap"],"argument":"VISUALIZATION","description":"Heatmap of important feature abundance at each time point in each group. [required]"},{"names":["--o-volatility-plots"],"argument":"VISUALIZATION","description":"Interactive volatility plots of MAZ and maturity scores, target (column) predictions, and the sample metadata. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"nmit","description":"Nonparametric microbial interdependence test","usage":"qiime longitudinal nmit [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table to use for microbial interdependence test. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [required]"},{"names":["--p-corr-method"],"argument":"TEXT Choices('kendall', 'pearson', 'spearman')","description":"The temporal correlation test to be applied."},{"names":["--p-dist-method"],"argument":"TEXT Choices('fro', 'nuc')","description":"Temporal distance method, see numpy.linalg.norm for details. [default: 'fro']"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix The resulting distance matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"pairwise-differences","description":"Paired difference testing and boxplots","usage":"qiime longitudinal pairwise-differences [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table to optionally use for paired comparisons. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"Numerical metadata or artifact column to test. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (e.g., Time) across which samples are paired. [required]"},{"names":["--p-state-1"],"argument":"TEXT","description":"Baseline state column value. [required]"},{"names":["--p-state-2"],"argument":"TEXT","description":"State column value to pair with baseline. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling=\"random\" to instead randomly select one member. [required]"},{"names":["--p-group-column"],"argument":"TEXT","description":"Metadata column on which to separate groups for comparison [optional]"},{"names":["--p-parametric","--p-no-parametric"],"argument":"","description":"Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests."},{"names":["--p-replicate-handling"],"argument":"TEXT Choices('error', 'random', 'drop')","description":"Choose how replicate samples are handled. If replicates are detected, \"error\" causes method to fail; \"drop\" will discard all replicated samples; \"random\" chooses one representative at random from among replicates. [default: 'error']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"pairwise-distances","description":"Paired pairwise distance testing and boxplots","usage":"qiime longitudinal pairwise-distances [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-group-column"],"argument":"TEXT","description":"Metadata column on which to separate groups for comparison [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (e.g., Time) across which samples are paired. [required]"},{"names":["--p-state-1"],"argument":"TEXT","description":"Baseline state column value. [required]"},{"names":["--p-state-2"],"argument":"TEXT","description":"State column value to pair with baseline. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling=\"random\" to instead randomly select one member. [required]"},{"names":["--p-parametric","--p-no-parametric"],"argument":"","description":"Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests."},{"names":["--p-replicate-handling"],"argument":"TEXT Choices('error', 'random', 'drop')","description":"Choose how replicate samples are handled. If replicates are detected, \"error\" causes method to fail; \"drop\" will discard all replicated samples; \"random\" chooses one representative at random from among replicates. [default: 'error']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"plot-feature-volatility","description":"Plot longitudinal feature volatility and importances","usage":"qiime longitudinal plot-feature-volatility [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table containing features found in importances. [required]"},{"names":["--i-importances"],"argument":"ARTIFACT FeatureData[Importance]","description":"Feature importance scores. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (time) variable information. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [optional]"},{"names":["--p-default-group-column"],"argument":"TEXT","description":"The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization)."},{"names":["--p-yscale"],"argument":"TEXT Choices('linear', 'pow', 'sqrt', 'log')","description":"y-axis scaling strategy to apply. [default: 'linear']"},{"names":["--p-importance-threshold"],"argument":"VALUE","description":"Filter feature table to exclude any features with an importance score less than this threshold."},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"volatility","description":"Generate interactive volatility plot","usage":"qiime longitudinal volatility [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table containing metrics. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (time) variable information. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [optional]"},{"names":["--p-default-group-column"],"argument":"TEXT","description":"The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization)."},{"names":["--p-default-metric"],"argument":"TEXT","description":"Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization). [optional]"},{"names":["--p-yscale"],"argument":"TEXT Choices('linear', 'pow', 'sqrt', 'log')","description":"y-axis scaling strategy to apply. [default: 'linear']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"metadata","description":"Plugin for working with Metadata.","usage":"qiime metadata [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"distance-matrix","description":"Create a distance matrix from a numeric Metadata column","usage":"qiime metadata distance-matrix [OPTIONS]","options":[{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Numeric metadata column to compute pairwise Euclidean distances from [required]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"merge","description":"Merge metadata","usage":"qiime metadata merge [OPTIONS]","options":[{"names":["--m-metadata1-file"],"argument":"METADATA...","description":"First metadata file to merge. [required]"},{"names":["--m-metadata2-file"],"argument":"METADATA...","description":"Second metadata file to merge. [required]"},{"names":["--o-merged-metadata"],"argument":"ARTIFACT","description":"ImmutableMetadata The merged metadata. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"shuffle-groups","description":"Shuffle values in a categorical sample metadata column.","usage":"qiime metadata shuffle-groups [OPTIONS]","options":[{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Categorical metadata column to shuffle. [required]"},{"names":["--p-n-columns"],"argument":"INTEGER","description":"The number of shuffled metadata columns to create."},{"names":["--p-md-column-name-prefix"],"argument":"TEXT","description":"Prefix to use in naming the shuffled metadata columns. [default: 'shuffled.grouping.']"},{"names":["--p-md-column-values-prefix"],"argument":"TEXT","description":"Prefix to use in naming the values in the shuffled metadata columns. [default: 'fake.group.']"},{"names":["--p-encode-sample-size","--p-no-encode-sample-size"],"argument":"","description":"If true, the sample size of each metadata group will be appended to the shuffled metadata column values."},{"names":["--o-shuffled-groups"],"argument":"ARTIFACT SampleData[ArtificialGrouping]","description":"Randomized metadata columns [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tabulate","description":"Interactively explore Metadata in an HTML table","usage":"qiime metadata tabulate [OPTIONS]","options":[{"names":["--m-input-file"],"argument":"METADATA...","description":"The metadata to tabulate. [required]"},{"names":["--p-page-size"],"argument":"INTEGER","description":"The maximum number of Metadata records to display per page [default: 100]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"phylogeny","description":"Plugin for generating and manipulating phylogenies.","usage":"qiime phylogeny [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"align-to-tree-mafft-fasttree","description":"Build a phylogenetic tree using fasttree and","usage":"qiime phylogeny align-to-tree-mafft-fasttree [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to be used for creating a fasttree based rooted phylogenetic tree. [required]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads. (Use `auto` to automatically use all available cores) This value is used when aligning the sequences and creating the tree with fasttree. [default: 1]"},{"names":["--p-mask-max-gap-frequency"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences."},{"names":["--p-mask-min-conservation"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences."},{"names":["--p-parttree","--p-no-parttree"],"argument":"","description":"This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. [default: False]"},{"names":["--o-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The aligned sequences. [required]"},{"names":["--o-masked-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The masked alignment. [required]"},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The unrooted phylogenetic tree."},{"names":["--o-rooted-tree"],"argument":"ARTIFACT","description":"Phylogeny[Rooted] The rooted phylogenetic tree. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"align-to-tree-mafft-iqtree","description":"Build a phylogenetic tree using iqtree and","usage":"qiime phylogeny align-to-tree-mafft-iqtree [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads. (Use 0 to automatically use all available cores This value is used when aligning the sequences and creating the tree with iqtree."},{"names":["--p-mask-max-gap-frequency"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences."},{"names":["--p-mask-min-conservation"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences."},{"names":["--p-substitution-model"],"argument":"TEXT","description":"Model of Nucleotide Substitution. If not provided, IQ-TREE will determine the best fit substitution model automatically."},{"names":["--p-fast","--p-no-fast"],"argument":"","description":"Fast search to resemble FastTree. [default: False]"},{"names":["--p-alrt"],"argument":"INTEGER","description":"Single branch test method. Number of bootstrap replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is required."},{"names":["--p-stop-iter"],"argument":"INTEGER","description":"Number of unsuccessful iterations to stop. 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[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"align-to-tree-mafft-raxml","description":"Build a phylogenetic tree using raxml and","usage":"qiime phylogeny align-to-tree-mafft-raxml [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads. (Use `all` to automatically use all available cores. This value is used when aligning the sequences and creating the tree with iqtree. [default: 1]"},{"names":["--p-mask-max-gap-frequency"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences."},{"names":["--p-mask-min-conservation"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences."},{"names":["--p-parttree","--p-no-parttree"],"argument":"","description":"This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. NOTE: if using this option, it is recomended that only the CAT-based substitution models of RAxML be considered for this pipeline."},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."},{"names":["--p-raxml-version"],"argument":"TEXT Choices('Standard', 'SSE3', 'AVX2')","description":"Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version."},{"names":["--o-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The aligned sequences. [required]"},{"names":["--o-masked-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The masked alignment. [required]"},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The unrooted phylogenetic tree."},{"names":["--o-rooted-tree"],"argument":"ARTIFACT","description":"Phylogeny[Rooted] The rooted phylogenetic tree. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fasttree","description":"Construct a phylogenetic tree with FastTree.","usage":"qiime phylogeny fasttree [OPTIONS]","options":[{"names":["--i-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned sequences to be used for phylogenetic reconstruction. [required]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads. Using more than one thread runs the non-deterministic variant of `FastTree` (`FastTreeMP`), and may result in a different tree than single-threading. See http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto` to automatically use all available cores) [default: 1]"},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The resulting phylogenetic tree."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-table","description":"Remove features from table if they're not","usage":"qiime phylogeny filter-table [OPTIONS]","options":[{"names":["--i-tree"],"argument":"ARTIFACT Phylogeny[Rooted | Unrooted]","description":"Tree where tip identifiers are the feature identifiers that should be retained in the table. [required]"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"Feature table that features should be filtered from."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-tree","description":"Remove features from tree based on metadata","usage":"qiime phylogeny filter-tree [OPTIONS]","options":[{"names":["--i-tree"],"argument":"ARTIFACT Phylogeny[Rooted¹ | Unrooted²]","description":"Tree that should be filtered [required]"},{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table which contains the identifier that should be retained in the tree"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Feature metadata to use with the 'where' statement or to select tips to be retained."},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. [optional]"},{"names":["--o-filtered-tree"],"argument":"ARTIFACT Phylogeny[Rooted¹ | Unrooted²]","description":"The resulting phylogenetic tree. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"iqtree","description":"Construct a phylogenetic tree with IQ-TREE.","usage":"qiime phylogeny iqtree [OPTIONS]","options":[{"names":["--i-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned sequences to be used for phylogenetic reconstruction. [required]"},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed. If not set, program defaults"},{"names":["--p-n-cores"],"argument":"NTHREADS","description":"The number of cores to use for parallel processing."},{"names":["--p-n-cores-max"],"argument":"NTHREADS","description":"Limits the maximum number of cores to be used when"},{"names":["--p-n-runs"],"argument":"INTEGER","description":"Number of indepedent runs. Multiple independent"},{"names":["--p-substitution-model"],"argument":"TEXT","description":"Model of Nucleotide Substitution."},{"names":["--p-n-init-pars-trees"],"argument":"INTEGER","description":"Number of initial parsimony trees."},{"names":["--p-n-top-init-trees"],"argument":"INTEGER","description":"Number of top initial trees."},{"names":["--p-n-best-retain-trees"],"argument":"INTEGER","description":"Number of best trees retained during search."},{"names":["--p-n-iter"],"argument":"INTEGER","description":"Fix number of iterations to stop."},{"names":["--p-stop-iter"],"argument":"INTEGER","description":"Number of unsuccessful iterations to stop."},{"names":["--p-perturb-nni-strength"],"argument":"NUMBER","description":"Perturbation strength for randomized NNI."},{"names":["--p-spr-radius"],"argument":"INTEGER","description":"Radius for parsimony SPR search."},{"names":["--p-allnni","--p-no-allnni"],"argument":"","description":"Perform more thorough NNI search. [default: False]"},{"names":["--p-fast","--p-no-fast"],"argument":"","description":"Fast search to resemble FastTree. [default: False]"},{"names":["--p-alrt"],"argument":"INTEGER","description":"Single branch test method. Number of bootstrap"},{"names":["--p-abayes","--p-no-abayes"],"argument":"","description":"Single branch test method. Approximate Bayes test."},{"names":["--p-lbp"],"argument":"INTEGER","description":"Single branch test method. Number of bootstrap"},{"names":["--p-safe","--p-no-safe"],"argument":"","description":"Safe likelihood kernel to avoid numerical"},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The resulting phylogenetic tree."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"iqtree-ultrafast-bootstrap","description":"Construct a phylogenetic tree with IQ-TREE","usage":"qiime phylogeny iqtree-ultrafast-bootstrap [OPTIONS]","options":[{"names":["--i-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned sequences to be used for phylogenetic reconstruction. [required]"},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed. If not set, program defaults"},{"names":["--p-n-cores"],"argument":"NTHREADS","description":"The number of cores to use for parallel processing."},{"names":["--p-n-cores-max"],"argument":"NTHREADS","description":"Limits the maximum number of cores to be used when"},{"names":["--p-n-runs"],"argument":"INTEGER","description":"Number of indepedent runs. Multiple independent"},{"names":["--p-substitution-model"],"argument":"TEXT","description":"Model of Nucleotide Substitution."},{"names":["--p-bootstrap-replicates"],"argument":"INTEGER","description":"The number of bootstrap searches to perform."},{"names":["--p-n-init-pars-trees"],"argument":"INTEGER","description":"Number of initial parsimony trees."},{"names":["--p-n-top-init-trees"],"argument":"INTEGER","description":"Number of top initial trees."},{"names":["--p-n-best-retain-trees"],"argument":"INTEGER","description":"Number of best trees retained during search."},{"names":["--p-stop-iter"],"argument":"INTEGER","description":"Number of unsuccessful iterations to stop."},{"names":["--p-perturb-nni-strength"],"argument":"NUMBER","description":"Perturbation strength for randomized NNI."},{"names":["--p-spr-radius"],"argument":"INTEGER","description":"Radius for parsimony SPR search."},{"names":["--p-n-max-ufboot-iter"],"argument":"INTEGER","description":"Maximum number of iterations."},{"names":["--p-n-ufboot-steps"],"argument":"INTEGER","description":"Number of iterations for UFBoot stopping rule."},{"names":["--p-min-cor-ufboot"],"argument":"NUMBER","description":"Minimum correlation coefficient."},{"names":["--p-ep-break-ufboot"],"argument":"NUMBER","description":"Epsilon value to break tie."},{"names":["--p-allnni","--p-no-allnni"],"argument":"","description":"Perform more thorough NNI search. [default: False]"},{"names":["--p-alrt"],"argument":"INTEGER","description":"Single branch test method."},{"names":["--p-abayes","--p-no-abayes"],"argument":"","description":"Single branch test method."},{"names":["--p-lbp"],"argument":"INTEGER","description":"Single branch test method."},{"names":["--p-bnni","--p-no-bnni"],"argument":"","description":"Optimize UFBoot trees by NNI on bootstrap alignment."},{"names":["--p-safe","--p-no-safe"],"argument":"","description":"Safe likelihood kernel to avoid numerical underflow."},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The resulting phylogenetic tree."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"midpoint-root","description":"Midpoint root an unrooted phylogenetic tree.","usage":"qiime phylogeny midpoint-root [OPTIONS]","options":[{"names":["--i-tree"],"argument":"ARTIFACT Phylogeny[Unrooted]","description":"The phylogenetic tree to be rooted. [required]"},{"names":["--o-rooted-tree"],"argument":"ARTIFACT","description":"Phylogeny[Rooted] The rooted phylogenetic tree. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"raxml","description":"Construct a phylogenetic tree with RAxML.","usage":"qiime phylogeny raxml [OPTIONS]","options":[{"names":["--i-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned sequences to be used for phylogenetic reconstruction. [required]"},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."},{"names":["--p-n-searches"],"argument":"INTEGER","description":"The number of independent maximum likelihood"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML. [default: 1]"},{"names":["--p-raxml-version"],"argument":"TEXT Choices('Standard', 'SSE3', 'AVX2')","description":"Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version."},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The resulting phylogenetic tree."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"raxml-rapid-bootstrap","description":"Construct a phylogenetic tree with bootstrap","usage":"qiime phylogeny raxml-rapid-bootstrap [OPTIONS]","options":[{"names":["--i-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned sequences to be used for phylogenetic reconstruction. [required]"},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."},{"names":["--p-rapid-bootstrap-seed"],"argument":"INTEGER","description":"Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen."},{"names":["--p-bootstrap-replicates"],"argument":"","description":"INTEGER"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML. [default: 1]"},{"names":["--p-raxml-version"],"argument":"TEXT Choices('Standard', 'SSE3', 'AVX2')","description":"Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version."},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The resulting phylogenetic tree."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"robinson-foulds","description":"Calculate Robinson-Foulds distance between","usage":"qiime phylogeny robinson-foulds [OPTIONS]","options":[{"names":["--i-trees"],"argument":"ARTIFACTS... List[Phylogeny[Rooted | Unrooted]]","description":"Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric. [required]"},{"names":["--p-labels"],"argument":"TEXT...","description":"Labels to use for the tree names in the distance"},{"names":["--p-missing-tips"],"argument":"TEXT Choices('error', 'intersect-all')","description":"How to handle tips that are not shared between trees. \"error\" will raise an error if the set of tips is not identical between all input trees. \"intersect-all\" will remove tips that are not shared between all trees before computing distances beteen trees. [default: 'error']"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix The distances between trees as a symmetric matrix."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"quality-control","description":"Plugin for quality control of feature and sequence data.","usage":"qiime quality-control [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"bowtie2-build","description":"Build bowtie2 index from reference sequences.","usage":"qiime quality-control bowtie2-build [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences used to build bowtie2 index."},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"Number of threads to launch.   [default: 1]"},{"names":["--o-database"],"argument":"ARTIFACT","description":"Bowtie2 index."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"decontam-identify","description":"Identify contaminants","usage":"qiime quality-control decontam-identify [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table which contaminate sequences will be identified from [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter [required]"},{"names":["--p-method"],"argument":"TEXT Choices('combined', 'frequency', 'prevalence')","description":"Select how to which method to id contaminants with; Prevalence: Utilizes control ASVs/OTUs to identify contaminants, Frequency: Utilizes sample concentration information to identify contaminants, Combined: Utilizes both Prevalence and Frequency methods when identifying contaminants [default: 'prevalence']"},{"names":["--p-freq-concentration-column"],"argument":"TEXT","description":"Input column name that has concentration information for the samples [optional]"},{"names":["--p-prev-control-column"],"argument":"TEXT","description":"Input column name containing experimental or control sample metadata [optional]"},{"names":["--p-prev-control-indicator"],"argument":"TEXT","description":"indicate the control sample identifier (e.g. \"control\" or \"blank\") [optional]"},{"names":["--o-decontam-scores"],"argument":"ARTIFACT FeatureData[DecontamScore]","description":"The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"decontam-identify-batches","description":"Identify contaminants in Batch Mode","usage":"qiime quality-control decontam-identify-batches [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table which contaminate sequences will be identified from [required]"},{"names":["--i-rep-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Representative Sequences table which contaminate seqeunces will be removed from [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter [required]"},{"names":["--p-split-column"],"argument":"TEXT","description":"input metadata columns that you wish to subset the ASV table byNote: Column names must be in quotes and delimited by a space [required]"},{"names":["--p-method"],"argument":"TEXT Choices('combined', 'frequency', 'prevalence')","description":"Select how to which method to id contaminants with; Prevalence: Utilizes control ASVs/OTUs to identify contaminants, Frequency: Utilizes sample concentration information to identify contaminants, Combined: Utilizes both Prevalence and Frequency methods when identifying contaminants [required]"},{"names":["--p-filter-empty-features","--p-no-filter-empty-features"],"argument":"","description":"If true, features which are not present in a split feature table are dropped. [optional]"},{"names":["--p-freq-concentration-column"],"argument":"TEXT","description":"Input column name that has concentration information for the samples [optional]"},{"names":["--p-prev-control-column"],"argument":"TEXT","description":"Input column name containing experimental or control sample metadata [optional]"},{"names":["--p-prev-control-indicator"],"argument":"TEXT","description":"indicate the control sample identifier (e.g. \"control\" or \"blank\") [optional]"},{"names":["--p-threshold"],"argument":"NUMBER","description":"Select threshold cutoff for decontam algorithm scores [default: 0.1]"},{"names":["--p-weighted","--p-no-weighted"],"argument":"","description":"weight the decontam scores by their associated read number [default: True]"},{"names":["--p-bin-size"],"argument":"NUMBER","description":"Select bin size for the histogram [default: 0.02]"},{"names":["--o-batch-subset-tables"],"argument":"ARTIFACTS... Collection[FeatureTable[Frequency]]","description":"Directory where feature tables split based on metadata and parameter split-column values should be written. [required]"},{"names":["--o-decontam-scores"],"argument":"ARTIFACTS... Collection[FeatureData[DecontamScore]]","description":"The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence [required]"},{"names":["--o-score-histograms"],"argument":"VISUALIZATION","description":"The vizulaizer histograms for all decontam score objects generated from the pipeline [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"decontam-remove","description":"Remove contaminants","usage":"qiime quality-control decontam-remove [OPTIONS]","options":[{"names":["--i-decontam-scores"],"argument":"ARTIFACT FeatureData[DecontamScore]","description":"Pre-feature decontam scores. [required]"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table from which contaminants will be removed. [required]"},{"names":["--i-rep-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Feature representative sequences from which contaminants will be removed. [required]"},{"names":["--p-threshold"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Decontam score threshold. Features with a score less than or equal to this threshold will be removed."},{"names":["--o-filtered-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table with contaminants removed. [required]"},{"names":["--o-filtered-rep-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Feature representative sequences with contaminants removed. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"decontam-score-viz","description":"Generate a histogram representation of the scores","usage":"qiime quality-control decontam-score-viz [OPTIONS]","options":[{"names":["--i-decontam-scores"],"argument":"ARTIFACTS... Collection[FeatureData[DecontamScore]]","description":"Output from decontam identify to be visualized"},{"names":["--i-table"],"argument":"ARTIFACTS... Collection[FeatureTable[Frequency]]","description":"Raw OTU/ASV table that was used as input to decontam-identify [required]"},{"names":["--i-rep-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Representative Sequences table which contaminate sequences will be removed from [optional]"},{"names":["--p-threshold"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Select threshold cutoff for decontam algorithm scores [default: 0.1]"},{"names":["--p-weighted","--p-no-weighted"],"argument":"","description":"weight the decontam scores by their associated read number [default: True]"},{"names":["--p-bin-size"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Select bin size for the histogram [default: 0.02]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-composition","description":"Evaluate expected vs. observed taxonomic composition of samples","usage":"qiime quality-control evaluate-composition [OPTIONS]","options":[{"names":["--i-expected-features"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Expected feature compositions [required]"},{"names":["--i-observed-features"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Observed feature compositions [required]"},{"names":["--p-depth"],"argument":"INTEGER","description":"Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [default: 7]"},{"names":["--p-plot-tar","--p-no-plot-tar"],"argument":"","description":"Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true positive features divided by the total number of observed features (TAR = true positives / (true positives + false positives)). [default: True]"},{"names":["--p-plot-tdr","--p-no-plot-tdr"],"argument":"","description":"Plot taxon detection rate (TDR) on score plot. TDR is the number of true positive features divided by the total number of expected features (TDR = true positives / (true positives + false negatives)). [default: True]"},{"names":["--p-plot-r-value","--p-no-plot-r-value"],"argument":"","description":"Plot expected vs. observed linear regression r value on score plot. [default: False]"},{"names":["--p-plot-r-squared","--p-no-plot-r-squared"],"argument":"","description":"Plot expected vs. observed linear regression r-squared value on score plot. [default: True]"},{"names":["--p-plot-bray-curtis","--p-no-plot-bray-curtis"],"argument":"","description":"Plot expected vs. observed Bray-Curtis dissimilarity scores on score plot. [default: False]"},{"names":["--p-plot-jaccard","--p-no-plot-jaccard"],"argument":"","description":"Plot expected vs. observed Jaccard distances scores on score plot. [default: False]"},{"names":["--p-plot-observed-features","--p-no-plot-observed-features"],"argument":"","description":"Plot observed features count on score plot."},{"names":["--p-plot-observed-features-ratio","--p-no-plot-observed-features-ratio"],"argument":"","description":"Plot ratio of observed:expected features on score plot. [default: True]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs. [optional]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-seqs","description":"Compare query (observed) vs. reference (expected) sequences.","usage":"qiime quality-control evaluate-seqs [OPTIONS]","options":[{"names":["--i-query-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to test for exclusion [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences to align against feature sequences"},{"names":["--p-show-alignments","--p-no-show-alignments"],"argument":"","description":"Option to plot pairwise alignments of query sequences and their top hits. [default: False]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-taxonomy","description":"Evaluate expected vs. observed taxonomic assignments","usage":"qiime quality-control evaluate-taxonomy [OPTIONS]","options":[{"names":["--i-expected-taxa"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Expected taxonomic assignments [required]"},{"names":["--i-observed-taxa"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Observed taxonomic assignments [required]"},{"names":["--i-feature-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Optional feature table containing relative frequency of each feature, used to weight accuracy scores by frequency. Must contain all features found in expected and/or observed taxa. Features found in the table but not the expected/observed taxa will be dropped prior to analysis. [optional]"},{"names":["--p-depth"],"argument":"INTEGER","description":"Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [required]"},{"names":["--p-require-exp-ids","--p-no-require-exp-ids"],"argument":"","description":"Require that all features found in observed taxa must be found in expected taxa or raise error."},{"names":["--p-require-obs-ids","--p-no-require-obs-ids"],"argument":"","description":"Require that all features found in expected taxa must be found in observed taxa or raise error."},{"names":["--p-sample-id"],"argument":"TEXT","description":"Optional sample ID to use for extracting frequency data from feature table, and for labeling accuracy results. If no sample-id is provided, feature frequencies are derived from the sum of all samples present in the feature table. [optional]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"exclude-seqs","description":"Exclude sequences by alignment","usage":"qiime quality-control exclude-seqs [OPTIONS]","options":[{"names":["--i-query-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to test for exclusion [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences to align against feature sequences [required]"},{"names":["--p-perc-identity"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0] [default: 0.97]"},{"names":["--p-evalue"],"argument":"NUMBER","description":"BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default. [optional]"},{"names":["--p-perc-query-aligned"],"argument":"NUMBER","description":"Percent of query sequence that must align to reference in order to be accepted as a hit."},{"names":["--p-threads"],"argument":"NTHREADS","description":"Number of threads to use. Only applies to vsearch method. [default: 1]"},{"names":["--o-sequence-hits"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Subset of feature sequences that align to reference sequences [required]"},{"names":["--o-sequence-misses"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Subset of feature sequences that do not align to reference sequences [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-reads","description":"Filter demultiplexed sequences by alignment to reference database.","usage":"qiime quality-control filter-reads [OPTIONS]","options":[{"names":["--i-database"],"argument":"ARTIFACT","description":"Bowtie2 indexed database."},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"Number of alignment threads to launch. [default: 1]"},{"names":["--p-mode"],"argument":"TEXT Choices('local', 'global')","description":"Bowtie2 alignment settings. See bowtie2 manual for more details. [default: 'local']"},{"names":["--p-ref-gap-open-penalty"],"argument":"","description":"INTEGER"},{"names":["--p-ref-gap-ext-penalty"],"argument":"","description":"INTEGER"},{"names":["--p-exclude-seqs","--p-no-exclude-seqs"],"argument":"","description":"Exclude sequences that align to reference. Set this option to False to exclude sequences that do not align to the reference database. [default: True]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"quality-filter","description":"Plugin for PHRED-based filtering and trimming.","usage":"qiime quality-filter [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"rescript","description":"Pipeline for reference sequence annotation and curation.","usage":"qiime rescript [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"cull-seqs","description":"Removes sequences that contain at least the specified number of degenerate bases and/or homopolymers of a given length.","usage":"qiime rescript cull-seqs [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence | RNASequence]","description":"DNA or RNA Sequences to be screened for removal based on degenerate base and homopolymer screening criteria. [required]"},{"names":["--p-num-degenerates"],"argument":"INTEGER","description":"Sequences with N, or more, degenerate bases will be removed."},{"names":["--p-homopolymer-length"],"argument":"INTEGER","description":"Sequences containing a homopolymer sequence of length N, or greater, will be removed."},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of concurrent processes to use while processing sequences."},{"names":["--o-clean-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting DNA sequences that pass degenerate base and homopolymer screening criteria. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"degap-seqs","description":"Remove gaps from DNA sequence alignments.","usage":"qiime rescript degap-seqs [OPTIONS]","options":[{"names":["--i-aligned-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned DNA Sequences to be degapped. [required]"},{"names":["--p-min-length"],"argument":"INTEGER","description":"Minimum length of sequence to be returned after degapping. [default: 1]"},{"names":["--o-degapped-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting unaligned (degapped) DNA sequences."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"dereplicate","description":"Dereplicate features with matching sequences and taxonomies.","usage":"qiime rescript dereplicate [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to be dereplicated [required]"},{"names":["--i-taxa"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic classifications of sequences to be dereplicated [required]"},{"names":["--p-mode"],"argument":"TEXT Choices('uniq', 'lca', 'majority', 'super')","description":"How to handle dereplication when sequences map to distinct taxonomies. \"uniq\" will retain all sequences with unique taxonomic affiliations. \"lca\" will find the least common ancestor among all taxa sharing a sequence. \"majority\" will find the most common taxonomic label associated with that sequence; note that in the event of a tie, \"majority\" will pick the winner arbitrarily. \"super\" finds the LCA consensus while giving preference to majority labels and collapsing substrings into superstrings. For example, when a more specific taxonomy does not contradict a less specific taxonomy, the more specific is chosen. That is, \"g__Faecalibacterium; s__prausnitzii\", will be preferred over \"g__Faecalibacterium; s__\""},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of computation threads to use (1 to 256)."},{"names":["--p-rank-handles"],"argument":"VALUES...","description":"Specifies the set of rank handles used to backfill missing ranks in the resulting dereplicated taxonomy."},{"names":["--p-derep-prefix","--p-no-derep-prefix"],"argument":"","description":"Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False]"},{"names":["--o-dereplicated-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"[required]"},{"names":["--o-dereplicated-taxa"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"edit-taxonomy","description":"Edit taxonomy strings with find and replace terms.","usage":"qiime rescript edit-taxonomy [OPTIONS]","options":[{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomy strings data to be edited. [required]"},{"names":["--m-replacement-map-file"],"argument":"","description":"METADATA"},{"names":["--m-replacement-map-column"],"argument":"COLUMN  MetadataColumn[Categorical]","description":"A tab-delimitad metadata file in which the strings in the 'id' column are replaced by the 'replacement-strings' in the second column. All strings in the 'id' column must be unique! [optional]"},{"names":["--p-search-strings"],"argument":"TEXT...","description":"Only used in conjuntion with 'replacement-strings'."},{"names":["--p-replacement-strings"],"argument":"TEXT...","description":"Only used in conjuntion with 'search-strings'."},{"names":["--p-use-regex","--p-no-use-regex"],"argument":"","description":"Toggle regular expressions. By default, only litereal substring matching is performed."},{"names":["--o-edited-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomy in which the original strings are replaced by user-supplied strings. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-classifications","description":"Interactively evaluate taxonomic classification accuracy.","usage":"qiime rescript evaluate-classifications [OPTIONS]","options":[{"names":["--i-expected-taxonomies"],"argument":"ARTIFACTS... List[FeatureData[Taxonomy]]","description":"True taxonomic labels for one more more sets of features. [required]"},{"names":["--i-observed-taxonomies"],"argument":"ARTIFACTS... List[FeatureData[Taxonomy]]","description":"Predicted classifications of same sets of features, input in same order as expected-taxonomies."},{"names":["--p-labels"],"argument":"TEXT...","description":"List of labels to use for labeling evaluation"},{"names":["--o-evaluation"],"argument":"VISUALIZATION","description":"Visualization of classification accuracy results."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-cross-validate","description":"Evaluate DNA sequence reference database via cross-validated taxonomic classification.","usage":"qiime rescript evaluate-cross-validate [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences to use for classifier training/testing. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Reference taxonomy to use for classifier training/testing. [required]"},{"names":["--p-k"],"argument":"INTEGER","description":"Number of stratified folds."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by the random number generator."},{"names":["--p-reads-per-batch"],"argument":"VALUE","description":"Number of reads to process in each batch. If \"auto\", this parameter is autoscaled to min( number of query sequences / n-jobs, 20000)."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]"},{"names":["--p-confidence"],"argument":"VALUE","description":"Confidence threshold for limiting taxonomic depth."},{"names":["--o-expected-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Expected taxonomic label for each input sequence. Taxonomic labels may be truncated due to k-fold CV and stratification. [required]"},{"names":["--o-observed-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Observed taxonomic label for each input sequence, predicted by cross-validation. [required]"},{"names":["--o-evaluation"],"argument":"VISUALIZATION","description":"Visualization of cross-validated accuracy results. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-fit-classifier","description":"Evaluate and train naive Bayes classifier on reference sequences.","usage":"qiime rescript evaluate-fit-classifier [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences to use for classifier training/testing. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Reference taxonomy to use for classifier training/testing. [required]"},{"names":["--p-reads-per-batch"],"argument":"VALUE","description":"Number of reads to process in each batch. If \"auto\", this parameter is autoscaled to min( number of query sequences / n-jobs, 20000)."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]"},{"names":["--p-confidence"],"argument":"VALUE","description":"Confidence threshold for limiting taxonomic depth."},{"names":["--o-classifier"],"argument":"ARTIFACT","description":"Trained naive Bayes taxonomic classifier. [required]"},{"names":["--o-evaluation"],"argument":"VISUALIZATION","description":"Visualization of classification accuracy results. [required]"},{"names":["--o-observed-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Observed taxonomic label for each input sequence, predicted by the trained classifier. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-seqs","description":"Compute summary statistics on sequence artifact(s).","usage":"qiime rescript evaluate-seqs [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACTS... List[FeatureData[Sequence]]","description":"One or more sets of sequences to evaluate. [required]"},{"names":["--p-labels"],"argument":"TEXT...","description":"List of labels to use for labeling evaluation results in the resulting visualization."},{"names":["--p-kmer-lengths"],"argument":"INTEGERS...","description":"Sequence kmer lengths to optionally use for entropy calculation."},{"names":["--p-subsample-kmers"],"argument":"PROPORTION","description":"Optionally subsample sequences prior to kmer entropy measurement."},{"names":["--p-palette"],"argument":"TEXT","description":"Color palette to use for plotting evaluation results."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-taxonomy","description":"Compute summary statistics on taxonomy artifact(s).","usage":"qiime rescript evaluate-taxonomy [OPTIONS]","options":[{"names":["--i-taxonomies"],"argument":"ARTIFACTS... List[FeatureData[Taxonomy]]","description":"One or more taxonomies to evaluate. [required]"},{"names":["--p-labels"],"argument":"TEXT...","description":"List of labels to use for labeling evaluation results in the resulting visualization."},{"names":["--p-rank-handle-regex"],"argument":"TEXT","description":"Regular expression indicating which taxonomic rank a label belongs to; this handle is stripped from the label prior to operating on the taxonomy. The net effect is that ambiguous or empty levels can be removed prior to comparison, enabling selection of taxonomies with more complete taxonomic information. For example, \"^[dkpcofgs]__\" will recognize greengenes or silva rank handles. [optional]"},{"names":["--o-taxonomy-stats"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"extract-seq-segments","description":"Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value.","usage":"qiime rescript extract-seq-segments [OPTIONS]","options":[{"names":["--i-input-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences from which matching shorter sequence segments (regions) can be extracted from. Sequences containing segments that match those from 'reference-segment-sequences' will have those segments extracted and written to file. [required]"},{"names":["--i-reference-segment-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequence segments that will be used to search for and extract matching segments from 'sequences'. [required]"},{"names":["--p-perc-identity"],"argument":"PROPORTION","description":"The percent identity at which clustering should be performed."},{"names":["--p-min-seq-len"],"argument":"INTEGER","description":"Minimum length of sequence allowed for searching."},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of computation threads to use (1 to 256)."},{"names":["--o-extracted-sequence-segments"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Extracted sequence segments from 'input-sequences' that succesfully aligned to 'reference-segment-sequences'. [required]"},{"names":["--o-unmatched-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences in 'input-sequences' that did not have matching sequence segments within 'reference-segment-sequences'. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-seqs-length","description":"Filter sequences by length.","usage":"qiime rescript filter-seqs-length [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to be filtered by length. [required]"},{"names":["--p-global-min"],"argument":"INTEGER","description":"The minimum length threshold for filtering all sequences."},{"names":["--p-global-max"],"argument":"INTEGER","description":"The maximum length threshold for filtering all sequences."},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of computation threads to use (1 to 256)."},{"names":["--o-filtered-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences that pass the filtering thresholds."},{"names":["--o-discarded-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences that fall outside the filtering thresholds. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-seqs-length-by-taxon","description":"Filter sequences by length and taxonomic group.","usage":"qiime rescript filter-seqs-length-by-taxon [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to be filtered by length. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic classifications of sequences to be filtered. [required]"},{"names":["--p-labels"],"argument":"TEXT...","description":"One or more taxonomic labels to use for conditional filtering. [required]"},{"names":["--p-min-lens"],"argument":"INTEGERS...","description":"Minimum length thresholds to use for filtering sequences associated with each label."},{"names":["--p-max-lens"],"argument":"INTEGERS...","description":"Maximum length thresholds to use for filtering sequences associated with each label."},{"names":["--p-global-min"],"argument":"INTEGER","description":"The minimum length threshold for filtering all sequences."},{"names":["--p-global-max"],"argument":"INTEGER","description":"The maximum length threshold for filtering all sequences."},{"names":["--o-filtered-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences that pass the filtering thresholds."},{"names":["--o-discarded-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences that fall outside the filtering thresholds. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-taxa","description":"Filter taxonomy by list of IDs or search criteria.","usage":"qiime rescript filter-taxa [OPTIONS]","options":[{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomy to filter. [required]"},{"names":["--m-ids-to-keep-file"],"argument":"METADATA...","description":"List of IDs to keep (as Metadata)."},{"names":["--p-include"],"argument":"TEXT...","description":"List of search terms. Taxa containing one or more of these terms will be retained."},{"names":["--p-exclude"],"argument":"TEXT...","description":"List of search terms. Taxa containing one or more of these terms will be excluded."},{"names":["--o-filtered-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"The filtered taxonomy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-gtdb-data","description":"Download, parse, and import SSU GTDB reference data.","usage":"qiime rescript get-gtdb-data [OPTIONS]","options":[{"names":["--p-version"],"argument":"TEXT Choices('202.0', '207.0', '214.0', '214.1')","description":"GTDB database version to download. [default: '214.1']"},{"names":["--p-domain"],"argument":"TEXT Choices('Both', 'Bacteria', 'Archaea')","description":"SSU sequence and taxonomy data to download from a given microbial domain from GTDB. 'Both' will fetch both bacterial and archaeal data. 'Bacteria' will only fetch bacterial data. 'Archaea' will only fetch archaeal data. This only applies to 'db-type SpeciesReps'. [default: 'Both']"},{"names":["--p-db-type"],"argument":"TEXT Choices('All', 'SpeciesReps')","description":"'All': All SSU data that pass the quality-control of GTDB, but are not clustered into representative species. 'SpeciesReps': SSU gene sequences identified within the set of representative species. Note: if 'All' is used, the 'domain' parameter will be ignored as GTDB does not maintain separate domain-level files for these non-clustered data. [default: 'SpeciesReps']"},{"names":["--o-gtdb-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"SSU GTDB reference taxonomy. [required]"},{"names":["--o-gtdb-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"SSU GTDB reference sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-ncbi-data","description":"Download, parse, and import NCBI sequences and taxonomies","usage":"qiime rescript get-ncbi-data [OPTIONS]","options":[{"names":["--p-query"],"argument":"TEXT","description":"Query on the NCBI Nucleotide database [optional]"},{"names":["--m-accession-ids-file"],"argument":"METADATA...","description":"List of accession ids for sequences in the NCBI Nucleotide database."},{"names":["--p-ranks"],"argument":"TEXT...","description":"List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy database."},{"names":["--p-rank-propagation","--p-no-rank-propagation"],"argument":"","description":"Propagate known ranks to missing ranks if true"},{"names":["--p-logging-level"],"argument":"TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL')","description":"Logging level"},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of concurrent download connections. More is faster until you run out of bandwidth. [default: 1]"},{"names":["--o-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences from the NCBI Nucleotide database [required]"},{"names":["--o-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomies from the NCBI Taxonomy database [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-ncbi-data-protein","description":"Download, parse, and import NCBI protein sequences and taxonomies","usage":"qiime rescript get-ncbi-data-protein [OPTIONS]","options":[{"names":["--p-query"],"argument":"TEXT","description":"Query on the NCBI Protein database [optional]"},{"names":["--m-accession-ids-file"],"argument":"METADATA...","description":"List of accession ids for sequences in the NCBI Protein database."},{"names":["--p-ranks"],"argument":"TEXT...","description":"List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy database."},{"names":["--p-rank-propagation","--p-no-rank-propagation"],"argument":"","description":"Propagate known ranks to missing ranks if true"},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of concurrent download connections. More is faster until you run out of bandwidth. [default: 1]"},{"names":["--o-sequences"],"argument":"ARTIFACT FeatureData[ProteinSequence]","description":"Sequences from the NCBI Protein database [required]"},{"names":["--o-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomies from the NCBI Taxonomy database [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-ncbi-genomes","description":"Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.","usage":"qiime rescript get-ncbi-genomes [OPTIONS]","options":[{"names":["--p-taxon"],"argument":"TEXT","description":"NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank. [required]"},{"names":["--p-assembly-source"],"argument":"TEXT Choices('refseq', 'genbank')","description":"Fetch only RefSeq or GenBank genome assemblies."},{"names":["--p-assembly-levels"],"argument":"TEXT... Choices('complete_genome', 'chromosome', 'scaffold', 'contig')","description":"Fetch only genome assemblies that are one of the specified assembly levels."},{"names":["--p-only-reference","--p-no-only-reference"],"argument":"","description":"Fetch only reference and representative genome assemblies. [default: True]"},{"names":["--p-tax-exact-match","--p-no-tax-exact-match"],"argument":"","description":"If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too. [default: False]"},{"names":["--p-page-size"],"argument":"INTEGER Range(20, 1000, inclusive_end=True)","description":"The maximum number of genome assemblies to return per request. If number of genomes to fetch is higher than this number, requests will be repeated until all assemblies are fetched. [default: 20]"},{"names":["--o-genome-assemblies"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Nucleotide sequences of requested genomes. [required]"},{"names":["--o-loci"],"argument":"ARTIFACT","description":"Loci features of requested genomes."},{"names":["--o-proteins"],"argument":"ARTIFACT GenomeData[Proteins]","description":"Protein sequences originating from requested genomes. [required]"},{"names":["--o-taxonomies"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomies of requested genomes. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-silva-data","description":"Download, parse, and import SILVA database.","usage":"qiime rescript get-silva-data [OPTIONS]","options":[{"names":["--p-include-species-labels","--p-no-include-species-labels"],"argument":"","description":"Include species rank labels in taxonomy output. Note: species-labels may not be reliable in all cases. [default: False]"},{"names":["--p-rank-propagation","--p-no-rank-propagation"],"argument":"","description":"If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for 'f__Pasteurellaceae; g__'then the 'f__' rank will be propagated to become: 'f__Pasteurellaceae; g__Pasteurellaceae'."},{"names":["--p-download-sequences","--p-no-download-sequences"],"argument":"","description":"Toggle whether or not to download and import the SILVA reference sequences associated with the release. Skipping the sequences is useful if you only want to download and parse the taxonomy, e.g., a local copy of the sequences already exists or for testing purposes. NOTE: if this option is used, a `silva-sequences` output is still created, but contains no data. [default: True]"},{"names":["--o-silva-sequences"],"argument":"ARTIFACT FeatureData[RNASequence]","description":"SILVA reference sequences. [required]"},{"names":["--o-silva-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"SILVA reference taxonomy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-unite-data","description":"Download and import UNITE reference data.","usage":"qiime rescript get-unite-data [OPTIONS]","options":[{"names":["--p-version"],"argument":"TEXT Choices('10.0', '9.0', '8.3', '8.2')","description":"UNITE version to download. [default: '10.0']"},{"names":["--p-taxon-group"],"argument":"TEXT Choices('fungi', 'eukaryotes')","description":"Download a database with only 'fungi' or including all 'eukaryotes'. [default: 'eukaryotes']"},{"names":["--p-cluster-id"],"argument":"TEXT Choices('99', '97', 'dynamic')","description":"Percent similarity at which sequences in the of database were clustered. [default: '99']"},{"names":["--p-singletons","--p-no-singletons"],"argument":"","description":"Include singleton clusters in the database."},{"names":["--o-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"UNITE reference taxonomy. [required]"},{"names":["--o-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"UNITE reference sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"merge-taxa","description":"Compare taxonomies and select the longest, highest scoring, or find the least common ancestor.","usage":"qiime rescript merge-taxa [OPTIONS]","options":[{"names":["--i-data"],"argument":"ARTIFACTS... List[FeatureData[Taxonomy]]","description":"Two or more feature taxonomies to be merged."},{"names":["--p-mode"],"argument":"TEXT Choices('len', 'lca', 'score', 'super', 'majority')","description":"How to merge feature taxonomies: \"len\" will select the taxonomy with the most elements (e.g., species level will beat genus level); \"lca\" will find the least common ancestor and report this consensus taxonomy; \"score\" will select the taxonomy with the highest score (e.g., confidence or consensus score). Note that \"score\" assumes that this score is always contained as the second column in a feature taxonomy dataframe. \"majority\" finds the LCA consensus while giving preference to majority labels. \"super\" finds the LCA consensus while giving preference to majority labels and collapsing substrings into superstrings. For example, when a more specific taxonomy does not contradict a less specific taxonomy, the more specific is chosen. That is, \"g__Faecalibacterium; s__prausnitzii\", will be preferred over \"g__Faecalibacterium; s__\" [default: 'len']"},{"names":["--p-rank-handle-regex"],"argument":"TEXT","description":"Regular expression indicating which taxonomic rank a label belongs to; this handle is stripped from the label prior to operating on the taxonomy. The net effect is that ambiguous or empty levels can be removed prior to comparison, enabling selection of taxonomies with more complete taxonomic information. For example, \"^[dkpcofgs]__\" will recognize greengenes or silva rank handles. Note that rank_handles are removed but not replaced; use the new_rank_handle parameter to replace the rank handles. [default: '^[dkpcofgs]__']"},{"names":["--p-new-rank-handles"],"argument":"VALUES...","description":"Specifies the set of rank handles to prepend to taxonomic labels at each rank."},{"names":["--p-unclassified-label"],"argument":"TEXT","description":"Specifies what label should be used for taxonomies that could not be resolved (when LCA modes are used)."},{"names":["--o-merged-data"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"orient-seqs","description":"Orient input sequences by comparison against reference.","usage":"qiime rescript orient-seqs [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to be oriented. [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences to orient against. If no reference is provided, all the sequences will be reverse complemented and all parameters will be ignored. [optional]"},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of computation threads to use (1 to 256)."},{"names":["--p-dbmask"],"argument":"TEXT Choices('none', 'dust', 'soft')","description":"Mask regions in the target database sequences using the dust method, or do not mask (none). When using soft masking, search commands become case sensitive."},{"names":["--p-relabel"],"argument":"TEXT","description":"Relabel sequences using the prefix string and a ticker (1, 2, 3, etc.) to construct the new headers. Use --sizeout to conserve the abundance annotations."},{"names":["--p-relabel-keep","--p-no-relabel-keep"],"argument":"","description":"When relabeling, keep the original identifier in the header after a space. [optional]"},{"names":["--p-relabel-md5","--p-no-relabel-md5"],"argument":"","description":"When relabeling, use the MD5 digest of the sequence as the new identifier. Use --sizeout to conserve the abundance annotations. [optional]"},{"names":["--p-relabel-self","--p-no-relabel-self"],"argument":"","description":"Relabel sequences using the sequence itself as a label. [optional]"},{"names":["--p-relabel-sha1","--p-no-relabel-sha1"],"argument":"","description":"When relabeling, use the SHA1 digest of the sequence as the new identifier. The probability of a collision is smaller than the MD5 algorithm."},{"names":["--p-sizein","--p-no-sizein"],"argument":"","description":"In de novo mode, abundance annotations (pattern `[>;]size=integer[;]`) present in sequence headers are taken into account. [optional]"},{"names":["--p-sizeout","--p-no-sizeout"],"argument":"","description":"Add abundance annotations to the output FASTA files. [optional]"},{"names":["--o-oriented-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query sequences in same orientation as top matching reference sequence. [required]"},{"names":["--o-unmatched-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query sequences that fail to match at least one reference sequence in either + or - orientation. This will be empty if no refrence is provided."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"parse-silva-taxonomy","description":"Generates a SILVA fixed-rank taxonomy.","usage":"qiime rescript parse-silva-taxonomy [OPTIONS]","options":[{"names":["--i-taxonomy-map"],"argument":"ARTIFACT FeatureData[SILVATaxidMap]","description":"SILVA taxonomy map. This file contains a mapping of the sequence accessions to the numeric taxonomy identifiers and species label information. The SILVA release filename is typically in the form of: 'taxmap_slv_ssu_ref_X.txt', or 'taxmap_slv_ssu_ref_nr_X.txt' where 'X' is the SILVA version number. [required]"},{"names":["--i-taxonomy-ranks"],"argument":"ARTIFACT FeatureData[SILVATaxonomy]","description":"SILVA taxonomy file. This file contains the taxonomic rank information for each numeric taxonomy identifier and the taxonomy. The SILVA filename typically takes the form of: 'tax_slv_ssu_X.txt', where 'X' is the SILVA version number. [required]"},{"names":["--i-taxonomy-tree"],"argument":"ARTIFACT","description":"Phylogeny[Rooted] SILVA hierarchical taxonomy tree. The SILVA release"},{"names":["--p-rank-propagation","--p-no-rank-propagation"],"argument":"","description":"If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for 'f__Pasteurellaceae; g__'then the 'f__' rank will be propagated to become: 'f__Pasteurellaceae; g__Pasteurellaceae'."},{"names":["--p-include-species-labels","--p-no-include-species-labels"],"argument":"","description":"Include species rank labels in taxonomy output. Note: species-labels may not be reliable in all cases. [default: False]"},{"names":["--o-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"The resulting fixed-rank formatted SILVA taxonomy."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"reverse-transcribe","description":"Reverse transcribe RNA to DNA sequences.","usage":"qiime rescript reverse-transcribe [OPTIONS]","options":[{"names":["--i-rna-sequences"],"argument":"ARTIFACT FeatureData","description":"RNA Sequences to reverse transcribe to DNA. [required]"},{"names":["--o-dna-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]","description":"Reverse-transcribed DNA sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"subsample-fasta","description":"Subsample an indicated number of sequences from a FASTA file.","usage":"qiime rescript subsample-fasta [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]","description":"Sequences to subsample from. [required]"},{"names":["--o-sample-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]","description":"Sample of original sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"trim-alignment","description":"Trim alignment based on provided primers or specific positions.","usage":"qiime rescript trim-alignment [OPTIONS]","options":[{"names":["--i-aligned-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned DNA sequences. [required]"},{"names":["--p-primer-fwd"],"argument":"TEXT","description":"Forward primer used to find the start position for alignment trimming. [optional]"},{"names":["--p-primer-rev"],"argument":"TEXT","description":"Reverse primer used to find the end position for alignment trimming. [optional]"},{"names":["--p-position-start"],"argument":"INTEGER","description":"Position within the alignment where the trimming will begin."},{"names":["--p-position-end"],"argument":"INTEGER","description":"Position within the alignment where the trimming will end."},{"names":["--o-trimmed-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Trimmed sequence alignment. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"sample-classifier","description":"Plugin for machine learning prediction of sample","usage":"qiime sample-classifier [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"classify-samples","description":"Train and test a cross-validated supervised","usage":"qiime sample-classifier classify-samples [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Categorical metadata column to use as prediction target. [required]"},{"names":["--p-test-size"],"argument":"PROPORTION","description":"Fraction of input samples to exclude from training set and use for classifier testing."},{"names":["--p-step"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"If optimize-feature-selection is True, step is the percentage of features to remove at each iteration."},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-estimator"],"argument":"{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}","description":"Estimator method to use for sample prediction."},{"names":["--p-optimize-feature-selection","--p-no-optimize-feature-selection"],"argument":"","description":"Automatically optimize input feature selection using recursive feature elimination."},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-palette"],"argument":"TEXT","description":"The color palette to use for plotting."},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Classifier]","description":"Trained sample estimator. [required]"},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy."},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[ClassifierPredictions]","description":"Predicted target values for each input sample."},{"names":["--o-model-summary"],"argument":"VISUALIZATION","description":"Summarized parameter and (if enabled) feature selection information for the trained estimator."},{"names":["--o-accuracy-results"],"argument":"VISUALIZATION","description":"Accuracy results visualization. [required]"},{"names":["--o-probabilities"],"argument":"ARTIFACT SampleData[Probabilities]","description":"Predicted class probabilities for each input sample. [required]"},{"names":["--o-heatmap"],"argument":"VISUALIZATION","description":"A heatmap of the top 50 most important features from the table. [required]"},{"names":["--o-training-targets"],"argument":"ARTIFACT SampleData[TrueTargets]","description":"Series containing true target values of train samples [required]"},{"names":["--o-test-targets"],"argument":"ARTIFACT SampleData[TrueTargets]","description":"Series containing true target values of test samples [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-samples-from-dist","description":"Run k-nearest-neighbors on a labeled distance","usage":"qiime sample-classifier classify-samples-from-dist [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix a distance matrix [required]"},{"names":["--p-k"],"argument":"INTEGER","description":"Number of nearest neighbors [default: 1]"},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel."},{"names":["--p-palette"],"argument":"TEXT","description":"The color palette to use for plotting."},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Categorical metadata column to use as prediction target. [required]"},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[ClassifierPredictions]","description":"leave one out predictions for each sample [required]"},{"names":["--o-accuracy-results"],"argument":"VISUALIZATION","description":"Accuracy results visualization. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-samples-ncv","description":"Nested cross-validated supervised learning","usage":"qiime sample-classifier classify-samples-ncv [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Categorical metadata column to use as prediction target. [required]"},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-estimator"],"argument":"{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}","description":"Estimator method to use for sample prediction."},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[ClassifierPredictions]","description":"Predicted target values for each input sample."},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy."},{"names":["--o-probabilities"],"argument":"ARTIFACT SampleData[Probabilities]","description":"Predicted class probabilities for each input sample."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"confusion-matrix","description":"Make a confusion matrix from sample classifier","usage":"qiime sample-classifier confusion-matrix [OPTIONS]","options":[{"names":["--i-predictions"],"argument":"ARTIFACT SampleData[ClassifierPredictions]","description":"Predicted values to plot on x axis. Should be predictions of categorical data produced by a sample classifier. [required]"},{"names":["--i-probabilities"],"argument":"ARTIFACT SampleData[Probabilities]","description":"Predicted class probabilities for each input sample."},{"names":["--m-truth-file","--m-truth-column"],"argument":"METADATA","description":"Metadata column (true values) to plot on y axis."},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fit-classifier","description":"Fit a supervised learning classifier.","usage":"qiime sample-classifier fit-classifier [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Numeric metadata column to use as prediction target."},{"names":["--p-step"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"If optimize-feature-selection is True, step is the percentage of features to remove at each iteration. [required]"},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-estimator"],"argument":"{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}","description":"Estimator method to use for sample prediction."},{"names":["--p-optimize-feature-selection","--p-no-optimize-feature-selection"],"argument":"","description":"Automatically optimize input feature selection using recursive feature elimination. [default: False]"},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Classifier]","description":"Trained sample classifier. [required]"},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fit-regressor","description":"Fit a supervised learning regressor.","usage":"qiime sample-classifier fit-regressor [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Numeric metadata column to use as prediction target. [required]"},{"names":["--p-step"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"If optimize-feature-selection is True, step is the percentage of features to remove at each iteration."},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-estimator"],"argument":"{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor[DecisionTree], AdaBoostRegressor[ExtraTrees], ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}","description":"Estimator method to use for sample prediction."},{"names":["--p-optimize-feature-selection","--p-no-optimize-feature-selection"],"argument":"","description":"Automatically optimize input feature selection using recursive feature elimination. [default: False]"},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata."},{"names":["--o-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Regressor]","description":"Trained sample regressor. [required]"},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"heatmap","description":"Generate heatmap of important features.","usage":"qiime sample-classifier heatmap [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--i-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Feature importances. [required]"},{"names":["--m-sample-metadata-file","--m-sample-metadata-column"],"argument":"METADATA","description":"Sample metadata column to use for sample labeling or grouping. [optional]"},{"names":["--m-feature-metadata-file","--m-feature-metadata-column"],"argument":"METADATA","description":"Feature metadata (e.g., taxonomy) to use for labeling features in the heatmap. [optional]"},{"names":["--p-feature-count"],"argument":"INTEGER","description":"Filter feature table to include top N most important features."},{"names":["--p-importance-threshold"],"argument":"NUMBER","description":"Filter feature table to include top N most important features."},{"names":["--p-group-samples","--p-no-group-samples"],"argument":"","description":"Group samples by sample metadata. [default: False]"},{"names":["--p-normalize","--p-no-normalize"],"argument":"","description":"Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table."},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'ignore']"},{"names":["--p-metric"],"argument":"TEXT","description":"Metrics exposed by seaborn"},{"names":["--p-method"],"argument":"TEXT","description":"Clustering methods exposed by seaborn"},{"names":["--p-cluster"],"argument":"TEXT Choices('both', 'features', 'none', 'samples')","description":"Specify which axes to cluster. [default: 'features']"},{"names":["--p-color-scheme"],"argument":"TEXT","description":"Color scheme for heatmap."},{"names":["--o-heatmap"],"argument":"VISUALIZATION","description":"Heatmap of important features. [required]"},{"names":["--o-filtered-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Filtered feature table containing data displayed in heatmap. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"metatable","description":"Convert (and merge) positive numeric metadata","usage":"qiime sample-classifier metatable [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction."},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Metadata file to convert to feature table. [required]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'ignore']"},{"names":["--p-missing-values"],"argument":"TEXT Choices('drop_samples', 'drop_features', 'error', 'fill')","description":"How to handle missing values (nans) in metadata."},{"names":["--p-drop-all-unique","--p-no-drop-all-unique"],"argument":"","description":"If True, columns that contain a unique value for every ID will be dropped. [default: False]"},{"names":["--o-converted-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Converted feature table [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"predict-classification","description":"Use trained classifier to predict target values","usage":"qiime sample-classifier predict-classification [OPTIONS]","options":[{"names":["--i-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Classifier]","description":"Sample classifier trained with fit_classifier."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel.   [default: 1]"},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[ClassifierPredictions]","description":"Predicted target values for each input sample."},{"names":["--o-probabilities"],"argument":"ARTIFACT SampleData[Probabilities]","description":"Predicted class probabilities for each input sample."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"predict-regression","description":"Use trained regressor to predict target values","usage":"qiime sample-classifier predict-regression [OPTIONS]","options":[{"names":["--i-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Regressor]","description":"Sample regressor trained with fit_regressor. [required]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel.   [default: 1]"},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[RegressorPredictions]","description":"Predicted target values for each input sample."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"regress-samples","description":"Train and test a cross-validated supervised","usage":"qiime sample-classifier regress-samples [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Numeric metadata column to use as prediction target. [required]"},{"names":["--p-test-size"],"argument":"PROPORTION","description":"Fraction of input samples to exclude from training set and use for classifier testing."},{"names":["--p-step"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"If optimize-feature-selection is True, step is the percentage of features to remove at each iteration."},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-estimator"],"argument":"{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor, ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}","description":"Estimator method to use for sample prediction."},{"names":["--p-optimize-feature-selection","--p-no-optimize-feature-selection"],"argument":"","description":"Automatically optimize input feature selection using recursive feature elimination."},{"names":["--p-stratify","--p-no-stratify"],"argument":"","description":"Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: False]"},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Regressor]","description":"Trained sample estimator. [required]"},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy. [required]"},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[RegressorPredictions]","description":"Predicted target values for each input sample. [required]"},{"names":["--o-model-summary"],"argument":"VISUALIZATION","description":"Summarized parameter and (if enabled) feature selection information for the trained estimator. [required]"},{"names":["--o-accuracy-results"],"argument":"VISUALIZATION","description":"Accuracy results visualization. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"regress-samples-ncv","description":"Nested cross-validated supervised learning","usage":"qiime sample-classifier regress-samples-ncv [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Numeric metadata column to use as prediction target."},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-estimator"],"argument":"{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor, ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}","description":"Estimator method to use for sample prediction."},{"names":["--p-stratify","--p-no-stratify"],"argument":"","description":"Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: False]"},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[RegressorPredictions]","description":"Predicted target values for each input sample. [required]"},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"scatterplot","description":"Make 2D scatterplot and linear regression of","usage":"qiime sample-classifier scatterplot [OPTIONS]","options":[{"names":["--i-predictions"],"argument":"ARTIFACT SampleData[RegressorPredictions]","description":"Predicted values to plot on y axis. Must be predictions of numeric data produced by a sample regressor. [required]"},{"names":["--m-truth-file","--m-truth-column"],"argument":"METADATA","description":"Metadata column (true values) to plot on x axis."},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"split-table","description":"Split a feature table into training and testing","usage":"qiime sample-classifier split-table [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction."},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Numeric metadata column to use as prediction target."},{"names":["--p-test-size"],"argument":"PROPORTION","description":"Fraction of input samples to exclude from training set and use for classifier testing."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-stratify","--p-no-stratify"],"argument":"","description":"Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: True]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-training-table"],"argument":"ARTIFACT FeatureTable","description":"Feature table containing training samples [required]"},{"names":["--o-test-table"],"argument":"ARTIFACT FeatureTable","description":"Feature table containing test samples [required]"},{"names":["--o-training-targets"],"argument":"ARTIFACT SampleData[TrueTargets]","description":"Series containing true target values of train samples"},{"names":["--o-test-targets"],"argument":"ARTIFACT SampleData[TrueTargets]","description":"Series containing true target values of test samples"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"summarize","description":"Summarize parameter and feature extraction","usage":"qiime sample-classifier summarize [OPTIONS]","options":[{"names":["--i-sample-estimator"],"argument":"","description":"ARTIFACT SampleEstimator[Classifier | Regressor] Sample estimator trained with fit_classifier or fit_regressor. [required]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"taxa","description":"Plugin for working with feature taxonomy annotations.","usage":"qiime taxa [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"barplot","description":"Visualize taxonomy with an interactive bar plot","usage":"qiime taxa barplot [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | PresenceAbsence]","description":"Feature table to visualize at various taxonomic levels. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. If no taxonomy is provided, the feature IDs will be used as labels. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata."},{"names":["--p-level-delimiter"],"argument":"TEXT","description":"Attempt to parse hierarchical taxonomic information from feature IDs by separating levels with this character. This parameter is ignored if a taxonomy is provided as input. [optional]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"collapse","description":"Collapse features by their taxonomy at the specified level","usage":"qiime taxa collapse [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table to be collapsed. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]"},{"names":["--p-level"],"argument":"INTEGER","description":"The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]"},{"names":["--o-collapsed-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-seqs","description":"Taxonomy-based feature sequence filter.","usage":"qiime taxa filter-seqs [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Feature sequences to be filtered. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic annotations for features in the provided feature sequences. All features in the feature sequences must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature sequences will be ignored. [required]"},{"names":["--p-include"],"argument":"TEXT","description":"One or more search terms that indicate which taxa should be included in the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional]"},{"names":["--p-exclude"],"argument":"TEXT","description":"One or more search terms that indicate which taxa should be excluded from the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional]"},{"names":["--p-query-delimiter"],"argument":"TEXT","description":"The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ',']"},{"names":["--p-mode"],"argument":"TEXT Choices('exact', 'contains')","description":"Mode for determining if a search term matches a taxonomic annotation. \"contains\" requires that the annotation has the term as a substring; \"exact\" requires that the annotation is a perfect match to a search term. [default: 'contains']"},{"names":["--o-filtered-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The taxonomy-filtered feature sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-table","description":"Taxonomy-based feature table filter.","usage":"qiime taxa filter-table [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency¹ | PresenceAbsence²]","description":"Feature table to be filtered. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored. [required]"},{"names":["--p-include"],"argument":"TEXT","description":"One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional]"},{"names":["--p-exclude"],"argument":"TEXT","description":"One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional]"},{"names":["--p-query-delimiter"],"argument":"TEXT","description":"The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations."},{"names":["--p-mode"],"argument":"TEXT Choices('exact', 'contains')","description":"Mode for determining if a search term matches a taxonomic annotation. \"contains\" requires that the annotation has the term as a substring; \"exact\" requires that the annotation is a perfect match to a search term. [default: 'contains']"},{"names":["--o-filtered-table"],"argument":"ARTIFACT FeatureTable[Frequency¹ | PresenceAbsence²]","description":"The taxonomy-filtered feature table. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"vsearch","description":"Plugin for clustering and dereplicating with vsearch.","usage":"qiime vsearch [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"cluster-features-closed-reference","description":"Closed-reference clustering of features.","usage":"qiime vsearch cluster-features-closed-reference [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT","description":"The sequences corresponding to the features in table. [required]"},{"names":["--i-table"],"argument":"ARTIFACT","description":"The feature table to be clustered. [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to use as cluster centroids. [required]"},{"names":["--p-perc-identity"],"argument":"","description":"The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required]"},{"names":["--p-strand"],"argument":"{'plus', 'both'}","description":"Search plus (i.e., forward) or both (i.e., forward and reverse complement) strands. [default: 'plus']"},{"names":["--p-threads"],"argument":"INTEGER","description":"The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1]"},{"names":["--o-clustered-table"],"argument":"ARTIFACT","description":"The table following clustering of features. [required]"},{"names":["--o-clustered-sequences"],"argument":"ARTIFACT","description":"The sequences representing clustered features, relabeled by the reference IDs. [required]"},{"names":["--o-unmatched-sequences"],"argument":"ARTIFACT","description":"The sequences which failed to match any reference sequences. This output maps to vsearch's --notmatched parameter. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cluster-features-de-novo","description":"De novo clustering of features.","usage":"qiime vsearch cluster-features-de-novo [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences corresponding to the features in table. [required]"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to be clustered. [required]"},{"names":["--p-strand"],"argument":"TEXT Choices('plus', 'both')","description":"Search plus (i.e., forward) or both (i.e., forward and reverse complement) strands. [default: 'plus']"},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of threads to use for computation. Passing 0 will launch one thread per CPU core."},{"names":["--o-clustered-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The table following clustering of features."},{"names":["--o-clustered-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences representing clustered features."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cluster-features-open-reference","description":"Open-reference clustering of features.","usage":"qiime vsearch cluster-features-open-reference [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT","description":"The sequences corresponding to the features in table. [required]"},{"names":["--i-table"],"argument":"ARTIFACT","description":"The feature table to be clustered. [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT","description":"The sequences to use as cluster centroids. [required]"},{"names":["--p-perc-identity"],"argument":"PROPORTION","description":"The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required]"},{"names":["--p-strand"],"argument":"{'plus', 'both'}","description":"Search plus (i.e., forward) or both (i.e., forward and reverse complement) strands. [default: 'plus']"},{"names":["--p-threads"],"argument":"INTEGER","description":"The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1]"},{"names":["--o-clustered-table"],"argument":"ARTIFACT","description":"The table following clustering of features. [required]"},{"names":["--o-clustered-sequences"],"argument":"ARTIFACT","description":"Sequences representing clustered features. [required]"},{"names":["--o-new-reference-sequences"],"argument":"ARTIFACT","description":"The new reference sequences. This can be used for subsequent runs of open-reference clustering for consistent definitions of features across open-reference feature tables. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"dereplicate-sequences","description":"Dereplicate sequences.","usage":"qiime vsearch dereplicate-sequences [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT SampleData","description":"|   SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]"},{"names":["--i-sequences"],"argument":"ARTIFACT SampleDataSequences","description":"|   SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]"},{"names":["--p-derep-prefix","--p-no-derep-prefix"],"argument":"","description":"Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False]"},{"names":["--p-min-seq-length"],"argument":"INTEGER","description":"Discard sequences shorter than this integer."},{"names":["--p-min-unique-size"],"argument":"INTEGER","description":"Discard sequences with a post-dereplication"},{"names":["--o-dereplicated-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The table of dereplicated sequences. [required]"},{"names":["--o-dereplicated-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The dereplicated sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fastq-stats","description":"Fastq stats with vsearch.","usage":"qiime vsearch fastq-stats [OPTIONS]","options":[{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of threads used for computation."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"merge-pairs","description":"Merge paired-end reads.","usage":"qiime vsearch merge-pairs [OPTIONS]","options":[{"names":["--i-demultiplexed-seqs"],"argument":"","description":"ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be merged."},{"names":["--p-truncqual"],"argument":"INTEGER","description":"Truncate sequences at the first base with the specified quality score value or lower."},{"names":["--p-minlen"],"argument":"INTEGER","description":"Sequences shorter than minlen after truncation are discarded."},{"names":["--p-maxns"],"argument":"INTEGER","description":"Sequences with more than maxns N characters are discarded."},{"names":["--p-allowmergestagger","--p-no-allowmergestagger"],"argument":"","description":"Allow merging of staggered read pairs."},{"names":["--p-minovlen"],"argument":"INTEGER","description":"Minimum length of the area of overlap between reads during merging."},{"names":["--p-maxdiffs"],"argument":"INTEGER","description":"Maximum number of mismatches in the area of overlap during merging."},{"names":["--p-minmergelen"],"argument":"INTEGER","description":"Minimum length of the merged read to be retained."},{"names":["--p-maxmergelen"],"argument":"INTEGER","description":"Maximum length of the merged read to be retained."},{"names":["--p-maxee"],"argument":"NUMBER","description":"Maximum number of expected errors in the merged read to be retained."},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of threads to use for computation."},{"names":["--o-merged-sequences"],"argument":"ARTIFACT SampleData[JoinedSequencesWithQuality]","description":"The merged sequences. [required]"},{"names":["--o-unmerged-sequences"],"argument":"ARTIFACT","description":"The unmerged paired-end reads. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"uchime-denovo","description":"De novo chimera filtering with vsearch.","usage":"qiime vsearch uchime-denovo [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The feature sequences to be chimera-checked."},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table (used for computing total feature abundances). [required]"},{"names":["--p-dn"],"argument":"NUMBER","description":"No vote pseudo-count, corresponding to the"},{"names":["--p-mindiffs"],"argument":"INTEGER","description":"Minimum number of differences per segment."},{"names":["--p-mindiv"],"argument":"NUMBER","description":"Minimum divergence from closest parent."},{"names":["--p-minh"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]"},{"names":["--p-xn"],"argument":"NUMBER Range(1.0, None, inclusive_start=False)","description":"No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]"},{"names":["--o-chimeras"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The chimeric sequences. [required]"},{"names":["--o-nonchimeras"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The non-chimeric sequences. [required]"},{"names":["--o-stats"],"argument":"ARTIFACT","description":"Summary statistics from chimera checking."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"uchime-ref","description":"Reference-based chimera filtering with","usage":"qiime vsearch uchime-ref [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The feature sequences to be chimera-checked."},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table (used for computing total feature abundances). [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The non-chimeric reference sequences. [required]"},{"names":["--p-dn"],"argument":"NUMBER","description":"No vote pseudo-count, corresponding to the"},{"names":["--p-mindiffs"],"argument":"INTEGER","description":"Minimum number of differences per segment."},{"names":["--p-mindiv"],"argument":"NUMBER","description":"Minimum divergence from closest parent."},{"names":["--p-minh"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]"},{"names":["--p-xn"],"argument":"NUMBER Range(1.0, None, inclusive_start=False)","description":"No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]"},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of threads to use for computation. Passing 0 will launch one thread per CPU core."},{"names":["--o-chimeras"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The chimeric sequences. [required]"},{"names":["--o-nonchimeras"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The non-chimeric sequences. [required]"},{"names":["--o-stats"],"argument":"ARTIFACT","description":"Summary statistics from chimera checking."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]}],"version":"q2cli version 2024.5.0"}
+{"name":"qiime","description":"Command line interface for QIIME 2","usage":"qiime [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"info","description":"Display information about current deployment.","usage":"qiime info [OPTIONS]","options":[{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tools","description":"Tools for working with QIIME 2 files.","usage":"qiime tools [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"cache-create","description":"Create an empty cache at the given location.","usage":"qiime tools cache-create [OPTIONS]","options":[{"names":["--cache"],"argument":"PATH","description":"Path to a nonexistent directory to be created as a cache."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cache-fetch","description":"Fetches an artifact out of a cache into a .qza.","usage":"qiime tools cache-fetch [OPTIONS]","options":[{"names":["--cache"],"argument":"DIRECTORY","description":"Path to an existing cache to load from.   [required]"},{"names":["--key"],"argument":"TEXT","description":"The key to the artifact being loaded.   [required]"},{"names":["--output-path"],"argument":"PATH","description":"Path to put the .qza we are loading the artifact into.   [required]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cache-garbage-collection","description":"Runs garbage collection on the cache at the specified location.","usage":"qiime tools cache-garbage-collection [OPTIONS]","options":[{"names":["--cache"],"argument":"DIRECTORY","description":"Path to an existing cache to run garbage collection on."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cache-import","description":"Imports data into an Artifact in the cache under a key.","usage":"qiime tools cache-import [OPTIONS]","options":[{"names":["--type"],"argument":"TEXT","description":"The semantic type of the artifact that will be created upon importing. Use `qiime tools list-types` to see what importable semantic types are available in the current deployment. [required]"},{"names":["--input-path"],"argument":"PATH","description":"Path to file or directory that should be imported. [required]"},{"names":["--cache"],"argument":"DIRECTORY","description":"Path to an existing cache to save into. [required]"},{"names":["--key"],"argument":"TEXT","description":"The key to save the artifact under (must be a valid Python identifier). [required]"},{"names":["--input-format"],"argument":"TEXT","description":"The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type. Use `qiime tools list-formats --importable` to see which formats of input data are importable."},{"names":["--validate-level"],"argument":"[min|max]","description":"How much to validate the imported data before creating the artifact. A value of \"max\" will generally read the entire file or directory, whereas \"min\" will not usually do so. [default: \"max\"]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cache-remove","description":"Removes a given key from a cache.","usage":"qiime tools cache-remove [OPTIONS]","options":[{"names":["--cache"],"argument":"DIRECTORY","description":"Path to an existing cache to remove the key from.   [required]"},{"names":["--key"],"argument":"TEXT","description":"The key to remove from the cache.   [required]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cache-status","description":"Checks the status of the cache.","usage":"qiime tools cache-status [OPTIONS]","options":[{"names":["--cache"],"argument":"DIRECTORY","description":"Path to an existing cache to check the status of."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cache-store","description":"Stores a .qza in the cache under a key.","usage":"qiime tools cache-store [OPTIONS]","options":[{"names":["--cache"],"argument":"DIRECTORY","description":"Path to an existing cache to save into. [required]"},{"names":["--artifact-path"],"argument":"FILE","description":"Path to a .qza to save into the cache. [required]"},{"names":["--key"],"argument":"TEXT","description":"The key to save the artifact under (must be a valid Python identifier). [required]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cast-metadata","description":"Designate metadata column types.","usage":"qiime tools cast-metadata [OPTIONS] METADATA...","options":[{"names":["--cast"],"argument":"COLUMN:TYPE","description":"Parameter for each metadata column that should be cast as a specified column type (supported types are as follows: categorical, numeric). The required formatting for this parameter is --cast COLUMN:TYPE, repeated for each column and the associated column type it should be cast to in the output. [required]"},{"names":["--ignore-extra"],"argument":"","description":"If this flag is enabled, cast parameters that do not correspond to any of the column names within the provided metadata will be ignored."},{"names":["--error-on-missing"],"argument":"","description":"If this flag is enabled, failing to include cast parameters for all columns in the provided metadata will result in an error."},{"names":["--output-file"],"argument":"FILE","description":"Path to file where the modified metadata should be written to."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"citations","description":"Print citations for a QIIME 2 result.","usage":"qiime tools citations [OPTIONS] ARTIFACT/VISUALIZATION","options":[{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"export","description":"Export data from a QIIME 2 Artifact or a Visualization","usage":"qiime tools export [OPTIONS]","options":[{"names":["--input-path"],"argument":"ARTIFACT/VISUALIZATION","description":"Path to file that should be exported [required]"},{"names":["--output-path"],"argument":"PATH","description":"Path to file or directory where data should be exported to [required]"},{"names":["--output-format"],"argument":"TEXT","description":"Format which the data should be exported as. This option cannot be used with Visualizations"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"extract","description":"Extract a QIIME 2 Artifact or Visualization archive.","usage":"qiime tools extract [OPTIONS]","options":[{"names":["--input-path"],"argument":"ARTIFACT/VISUALIZATION","description":"Path to file that should be extracted [required]"},{"names":["--output-path"],"argument":"DIRECTORY","description":"Directory where archive should be extracted to"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"import","description":"Import data into a new QIIME 2 Artifact.","usage":"qiime tools import [OPTIONS]","options":[{"names":["--type"],"argument":"TEXT","description":"The semantic type of the artifact that will be created upon importing. Use `qiime tools list-types` to see what importable semantic types are available in the current deployment. [required]"},{"names":["--input-path"],"argument":"PATH","description":"Path to file or directory that should be imported. [required]"},{"names":["--output-path"],"argument":"ARTIFACT","description":"Path where output artifact should be written. [required]"},{"names":["--input-format"],"argument":"TEXT","description":"The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type. Use `qiime tools list-formats --importable` to see which formats of input data are importable."},{"names":["--validate-level"],"argument":"[min|max]","description":"How much to validate the imported data before creating the artifact. A value of \"max\" will generally read the entire file or directory, whereas \"min\" will not usually do so. [default: \"max\"]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"inspect-metadata","description":"Inspect columns available in metadata.","usage":"qiime tools inspect-metadata [OPTIONS] METADATA...","options":[{"names":["--tsv","--no-tsv"],"argument":"","description":"Print as machine-readable TSV instead of text."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"list-formats","description":"List the available formats.","usage":"qiime tools list-formats [OPTIONS] [QUERIES]...","options":[{"names":["--importable"],"argument":"","description":"List the importable formats."},{"names":["--exportable"],"argument":"","description":"List the exportable formats."},{"names":["--strict"],"argument":"","description":"Show only exact matches for the format argument(s)."},{"names":["--tsv"],"argument":"","description":"Print as machine readable tab-separated values."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"list-types","description":"List the available semantic types.","usage":"qiime tools list-types [OPTIONS] [QUERIES]...","options":[{"names":["--strict"],"argument":"","description":"Show only exact matches for the type argument(s)."},{"names":["--tsv"],"argument":"","description":"Print as machine readable tab-separated values."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"peek","description":"Take a peek at a QIIME 2 Artifact or Visualization.","usage":"qiime tools peek [OPTIONS] ARTIFACT/VISUALIZATION","options":[{"names":["--tsv","--no-tsv"],"argument":"","description":"Print as machine-readable tab-separated values."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"replay-citations","description":"Reports all citations from a QIIME 2 Artifact...","usage":"qiime tools replay-citations [OPTIONS]","options":[{"names":["--in-fp"],"argument":"TEXT","description":"filepath to a QIIME 2 Archive (.qza or .qzv) or directory of Archives [required]"},{"names":["--recurse","--no-recurse"],"argument":"","description":"if in-fp is a directory, will also search sub-directories when finding Archives to parse [default: no-recurse]"},{"names":["--deduplicate","--no-deduplicate"],"argument":"","description":"If deduplicate, duplicate citations will be removed heuristically, e.g. by comparing DOI fields. This greatly reduces manual curation of reference lists, but introduces a small risk of reference loss. [default: deduplicate]"},{"names":["--suppress-header","--no-suppress-header"],"argument":"","description":"do not write header/footer blocks in the output script"},{"names":["--verbose","--no-verbose"],"argument":"","description":"print status messages to stdout while processing"},{"names":["--out-fp"],"argument":"PATH","description":"the filepath where your bibtex file should be written"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"replay-provenance","description":"Replay provenance from a QIIME 2 Artifact...","usage":"qiime tools replay-provenance [OPTIONS]","options":[{"names":["--in-fp"],"argument":"TEXT","description":"filepath to a QIIME 2 Archive (.qza or .qzv) or directory of Archives [required]"},{"names":["--recurse","--no-recurse"],"argument":"","description":"if in-fp is a directory, will also search sub-directories when finding Archives to parse [default: no-recurse]"},{"names":["--usage-driver"],"argument":"[python3|cli]","description":"the target interface for your replay script [default: cli]"},{"names":["--validate-checksums","--no-validate-checksums"],"argument":"","description":"check that replayed archives are intact and uncorrupted"},{"names":["--parse-metadata","--no-parse-metadata"],"argument":"","description":"parse the original metadata captured in provenance for review or replay [default: parse-metadata]"},{"names":["--use-recorded-metadata","--no-use-recorded-metadata"],"argument":"","description":"re-use the original metadata captured in provenance"},{"names":["--suppress-header","--no-suppress-header"],"argument":"","description":"do not write header/footer blocks in the output script"},{"names":["--verbose","--no-verbose"],"argument":"","description":"print status messages to stdout while processing"},{"names":["--dump-recorded-metadata","--no-dump-recorded-metadata"],"argument":"","description":"write the original metadata captured in provenance to disk in the --metadata-out-dir directory"},{"names":["--metadata-out-dir"],"argument":"TEXT","description":"the directory where captured study metadata should be written if --dump-recorded-metadata. This often produces many outputs, so a dedicated directory should generally be used. Creates the directory if it does not already exist. By default, metadata is written to `${PWD}/recorded_metadata/`"},{"names":["--out-fp"],"argument":"PATH","description":"the filepath where your replay script should be written"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"replay-supplement","description":"Produces a zipfile package of useful...","usage":"qiime tools replay-supplement [OPTIONS]","options":[{"names":["--in-fp"],"argument":"TEXT","description":"filepath to a QIIME 2 Archive or directory of Archives"},{"names":["--recurse","--no-recurse"],"argument":"","description":"if in-fp is a directory, will also search sub-directories when finding .qza/.qzv files to parse [default: no-recurse]"},{"names":["--deduplicate","--no-deduplicate"],"argument":"","description":"If deduplicate, duplicate citations will be removed heuristically, e.g. by comparing DOI fields. This greatly reduces manual curation of reference lists, but introduces a small risk of reference loss. 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[default: html]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"dev","description":"Utilities for developers and advanced users.","usage":"qiime dev [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"assert-result-data","description":"Assert expression in Result.","usage":"qiime dev assert-result-data [OPTIONS] ARTIFACT/VISUALIZATION","options":[{"names":["--zip-data-path"],"argument":"TEXT","description":"The path within the zipped Result's data/ directory"},{"names":["--expression"],"argument":"TEXT","description":"The Python regular expression to match. [required]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"assert-result-type","description":"Assert Result is a specific type.","usage":"qiime dev assert-result-type [OPTIONS] ARTIFACT/VISUALIZATION","options":[{"names":["--qiime-type"],"argument":"TEXT","description":"QIIME 2 data type. [required]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"export-default-theme","description":"Export the default settings.","usage":"qiime dev export-default-theme [OPTIONS]","options":[{"names":["--output-path"],"argument":"FILE","description":"Path to output the config to [required]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"import-theme","description":"Install new command line theme.","usage":"qiime dev import-theme [OPTIONS]","options":[{"names":["--theme"],"argument":"FILE","description":"Path to file containing new theme info [required]"},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"refresh-cache","description":"Refresh CLI cache.","usage":"qiime dev refresh-cache [OPTIONS]","options":[{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"reset-theme","description":"Reset command line theme to default.","usage":"qiime dev reset-theme [OPTIONS]","options":[{"names":["--yes"],"argument":"","description":"--help Show this message and exit."}]}]},{"name":"alignment","description":"Plugin for generating and manipulating alignments.","usage":"qiime alignment [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"mafft","description":"De novo multiple sequence alignment with MAFFT","usage":"qiime alignment mafft [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to be aligned. [required]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads. (Use `auto` to automatically use all available cores) [default: 1]"},{"names":["--p-parttree","--p-no-parttree"],"argument":"","description":"This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default [default: False]"},{"names":["--o-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The aligned sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. 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[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"assembly","description":"QIIME 2 plugin for (meta)genome assembly.","usage":"qiime assembly [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--show-hidden-actions"],"argument":"","description":"This plugin has hidden actions with names starting with '_'. These are generally called internally by pipelines. 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[optional]"},{"names":["--p-k-max"],"argument":"INTEGER","description":"Maximum kmer size (<= 255), must be odd number. Overrides k-list. [optional]"},{"names":["--p-k-step"],"argument":"INTEGER","description":"Increment of kmer size of each iteration (<= 28), must be even number. Overrides k-list. [optional]"},{"names":["--p-no-mercy","--p-no-no-mercy"],"argument":"","description":"Do not add mercy kmers. [default: False]"},{"names":["--p-bubble-level"],"argument":"INTEGER","description":"Intensity of bubble merging, 0 to disable."},{"names":["--p-prune-level"],"argument":"INTEGER","description":"Strength of low depth pruning. [default: 2]"},{"names":["--p-prune-depth"],"argument":"INTEGER","description":"Remove unitigs with avg kmer depth less than this value."},{"names":["--p-disconnect-ratio"],"argument":"PROPORTION","description":"Disconnect unitigs if its depth is less than this ratio times the total depth of itself and its siblings. 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[default: False]"},{"names":["--p-kmin-1pass","--p-no-kmin-1pass"],"argument":"","description":"Use 1pass mode to build SdBG of k-min."},{"names":["--p-memory"],"argument":"NUMBER","description":"Max memory in byte to be used in SdBG construction"},{"names":["--p-mem-flag"],"argument":"INTEGER","description":"SdBG builder memory mode. 0: minimum; 1: moderate; others: use all memory specified by '-m/--memory'."},{"names":["--p-num-cpu-threads"],"argument":"INTEGER","description":"Number of CPU threads. [default: 1]"},{"names":["--p-no-hw-accel","--p-no-no-hw-accel"],"argument":"","description":"Run MEGAHIT without BMI2 and POPCNT hardware instructions. [default: False]"},{"names":["--p-min-contig-len"],"argument":"INTEGER","description":"Minimum length of contigs to output. [default: 200]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the contigs into."},{"names":["--p-coassemble"],"argument":"VALUE","description":"Co-assemble reads into contigs from all samples."},{"names":["--o-contigs"],"argument":"ARTIFACT","description":"The resulting assembled contigs. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"assemble-spades","description":"Assemble contigs using SPAdes.","usage":"qiime assembly assemble-spades [OPTIONS]","options":[{"names":["--i-seqs"],"argument":"ARTIFACT","description":"The paired- or single-end sequences to be assembled. [required]"},{"names":["--p-isolate","--p-no-isolate"],"argument":"","description":"This flag is highly recommended for high-coverage isolate and multi-cell data. [default: False]"},{"names":["--p-sc","--p-no-sc"],"argument":"","description":"This flag is required for MDA (single-cell) data."},{"names":["--p-meta","--p-no-meta"],"argument":"","description":"This flag is required for metagenomic data. This option is only supported in combination with paired-end reads. [default: False]"},{"names":["--p-bio","--p-no-bio"],"argument":"","description":"This flag is required for biosyntheticSPAdes mode."},{"names":["--p-corona","--p-no-corona"],"argument":"","description":"This flag is required for coronaSPAdes mode."},{"names":["--p-plasmid","--p-no-plasmid"],"argument":"","description":"Runs plasmidSPAdes pipeline for plasmid detection."},{"names":["--p-metaviral","--p-no-metaviral"],"argument":"","description":"Runs metaviralSPAdes pipeline for virus detection."},{"names":["--p-metaplasmid","--p-no-metaplasmid"],"argument":"","description":"Runs metaplasmidSPAdes pipeline for plasmid detection in metagenomic datasets (equivalent for --meta --plasmid). [default: False]"},{"names":["--p-only-assembler","--p-no-only-assembler"],"argument":"","description":"Runs only assembling (without read error correction). [default: False]"},{"names":["--p-careful","--p-no-careful"],"argument":"","description":"Tries to reduce number of mismatches and short indels. [default: False]"},{"names":["--p-disable-rr","--p-no-disable-rr"],"argument":"","description":"Disables repeat resolution stage of assembling."},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of threads."},{"names":["--p-memory"],"argument":"INTEGER","description":"RAM limit for SPAdes in Gb."},{"names":["--p-k"],"argument":"VALUES...","description":"List of k-mer sizes (must be odd and less than 128). [default: ['auto']]"},{"names":["--p-cov-cutoff"],"argument":"VALUES...","description":"Coverage cutoff value (a positive float number, or 'auto', or 'off')."},{"names":["--p-phred-offset"],"argument":"TEXT Choices('auto-detect', '33', '64')","description":"PHRED quality offset in the input reads (33 or 64)."},{"names":["--p-debug","--p-no-debug"],"argument":"","description":"Runs SPAdes in debug mode. 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Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"collate-contigs","description":"Collate contigs","usage":"qiime assembly collate-contigs [OPTIONS]","options":[{"names":["--i-contigs"],"argument":"ARTIFACTS...","description":"A collection of contigs to be collated. [required]"},{"names":["--o-collated-contigs"],"argument":"ARTIFACT","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. 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Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-contigs","description":"Evaluate quality of the assembled contigs using metaQUAST.","usage":"qiime assembly evaluate-contigs [OPTIONS]","options":[{"names":["--i-contigs"],"argument":"ARTIFACT","description":"Assembled contigs to be analyzed. [required]"},{"names":["--i-reads"],"argument":"ARTIFACT","description":"Original single- or paired-end reads."},{"names":["--i-references"],"argument":"ARTIFACTS...","description":"Reference genomes to align the assembled contigs against. [optional]"},{"names":["--i-mapped-reads"],"argument":"ARTIFACT SampleData[AlignmentMap]","description":"Reads-to-contigs alignment maps (alternative to 'reads').directly. [optional]"},{"names":["--p-min-contig"],"argument":"INTEGER","description":"Lower threshold for contig length."},{"names":["--p-threads"],"argument":"INTEGER","description":"Maximum number of parallel jobs."},{"names":["--p-k-mer-stats","--p-no-k-mer-stats"],"argument":"","description":"Compute k-mer-based quality metrics (recommended for large genomes). This may significantly increase memory and time consumption on large genomes."},{"names":["--p-k-mer-size"],"argument":"INTEGER","description":"Size of k used in k-mer-stats."},{"names":["--p-memory-efficient","--p-no-memory-efficient"],"argument":"","description":"Significantly reduce memory consumption for large genomes. Forces one separate thread per each assembly and each chromosome. [default: False]"},{"names":["--p-min-alignment"],"argument":"INTEGER","description":"Minimum length of alignment (in bp)."},{"names":["--p-min-identity"],"argument":"NUMBER","description":"Minimum percent identity considered as proper alignment."},{"names":["--p-ambiguity-usage"],"argument":"{none, one, all}","description":"Way of processing equally good alignments of a contig that are likely repeats. 'none', skips these alignments. 'one', takes the very best alignment. 'all', uses all alignments, but san cause a significant increase of # mismatches."},{"names":["--p-no-icarus","--p-no-no-icarus"],"argument":"","description":"Do not draw Icarus visualizations. This option is useful when evaluating large genomes across multiple samples, as this step can be very time-consuming."},{"names":["--p-contig-thresholds"],"argument":"INTEGERS...","description":"Range(0, None) List of contig length thresholds."},{"names":["--p-ambiguity-score"],"argument":"NUMBER","description":"Range(0.8, 1.0) Score for defining equally good alignments of a"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"generate-reads","description":"Simulate NGS reads using InSilicoSeq.","usage":"qiime assembly generate-reads [OPTIONS]","options":[{"names":["--i-genomes"],"argument":"ARTIFACT","description":"Input genome(s) from which the reads will originate. If the genomes are not provided, they will be fetched from NCBI based on the \"ncbi\" and \"n-genomes-ncbi\" parameters. [optional]"},{"names":["--p-sample-names"],"argument":"TEXT...","description":"List of sample names that should be generated."},{"names":["--p-n-genomes"],"argument":"INTEGER","description":"How many genomes will be used for the simulation."},{"names":["--p-ncbi"],"argument":"TEXT... '{bacteria, viruses, archaea}'","description":"Download input genomes from NCBI. Can be bacteria, viruses, archaea or a combination of the three."},{"names":["--p-n-genomes-ncbi"],"argument":"INTEGERS...","description":"How many genomes will be downloaded from NCBI."},{"names":["--p-abundance"],"argument":"{uniform, halfnormal, exponential, lognormal, zero-inflated-lognormal, off}","description":"Abundance distribution."},{"names":["--p-coverage"],"argument":"{halfnormal, exponential, lognormal, zero-inflated-lognormal, off}","description":"Coverage distribution."},{"names":["--p-n-reads"],"argument":"INTEGER","description":"Number of reads to generate."},{"names":["--p-mode"],"argument":"{kde, basic, perfect}","description":"Error model. If not specified, using kernel density estimation. [default: 'kde']"},{"names":["--p-model"],"argument":"{HiSeq, NovaSeq, MiSeq}","description":"Error model. Use either of the precomputed models when --mode set to 'kde'. [default: 'HiSeq']"},{"names":["--p-gc-bias","--p-no-gc-bias"],"argument":"","description":"If set, may fail to sequence reads with abnormal GC content. [default: False]"},{"names":["--p-cpus"],"argument":"INTEGER","description":"Number of cpus to use."},{"names":["--p-debug","--p-no-debug"],"argument":"","description":"Enable debug logging. [default: False]"},{"names":["--p-seed"],"argument":"INTEGER","description":"Seed for all the random number generators."},{"names":["--o-reads"],"argument":"ARTIFACT","description":"Simulated paired-end reads. [required]"},{"names":["--o-template-genomes"],"argument":"ARTIFACT","description":"Genome sequences from which the reads were generated. [required]"},{"names":["--o-abundances"],"argument":"ARTIFACT","description":"Abundances of genomes from which thereads were generated. If \"coverage\" parameter was set, this table becomes coverage distribution per sample."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"index-contigs","description":"Index contigs using Bowtie2.","usage":"qiime assembly index-contigs [OPTIONS]","options":[{"names":["--i-contigs"],"argument":"ARTIFACT","description":"Contigs to be indexed. [required]"},{"names":["--p-large-index","--p-no-large-index"],"argument":"","description":"Force generated index to be 'large', even if ref has fewer than 4 billion nucleotides."},{"names":["--p-debug","--p-no-debug"],"argument":"","description":"Use the debug binary; slower, assertions enabled."},{"names":["--p-sanitized","--p-no-sanitized"],"argument":"","description":"Use sanitized binary; slower, uses ASan and/or UBSan. [default: False]"},{"names":["--p-verbose","--p-no-verbose"],"argument":"","description":"Log the issued command. 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[default: 0.1]"},{"names":["--p-indels","--p-no-indels"],"argument":"","description":"Allow insertions or deletions of bases when matching adapters."},{"names":["--p-times"],"argument":"INTEGER","description":"Remove multiple occurrences of an adapter if it is repeated, up to `times` times."},{"names":["--p-overlap"],"argument":"INTEGER","description":"Require at least `overlap` bases of overlap between read and adapter for an adapter to be found."},{"names":["--p-match-read-wildcards","--p-no-match-read-wildcards"],"argument":"","description":"Interpret IUPAC wildcards (e.g., N) in reads."},{"names":["--p-match-adapter-wildcards","--p-no-match-adapter-wildcards"],"argument":"","description":"Interpret IUPAC wildcards (e.g., N) in adapters."},{"names":["--p-minimum-length"],"argument":"INTEGER","description":"Discard reads shorter than specified value. Note,"},{"names":["--p-discard-untrimmed","--p-no-discard-untrimmed"],"argument":"","description":"Discard reads in which no adapter was found."},{"names":["--p-max-expected-errors"],"argument":"NUMBER","description":"Discard reads that exceed maximum expected erroneous nucleotides."},{"names":["--p-max-n"],"argument":"NUMBER","description":"Discard reads with more than COUNT N bases. If interpreted as a fraction of the read length."},{"names":["--p-quality-cutoff-5end"],"argument":"INTEGER","description":"Trim nucleotides with Phred score quality lower than threshold from 5 prime end."},{"names":["--p-quality-cutoff-3end"],"argument":"INTEGER","description":"Trim nucleotides with Phred score quality lower than threshold from 3 prime end."},{"names":["--p-quality-base"],"argument":"INTEGER","description":"How the Phred score is encoded (33 or 64)."},{"names":["--o-trimmed-sequences"],"argument":"ARTIFACT","description":"The resulting trimmed sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"trim-single","description":"Find and remove adapters in demultiplexed single-end sequences.","usage":"qiime cutadapt trim-single [OPTIONS]","options":[{"names":["--i-demultiplexed-sequences"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The single-end sequences to be trimmed. [required]"},{"names":["--p-cores"],"argument":"NTHREADS","description":"Number of CPU cores to use."},{"names":["--p-adapter"],"argument":"TEXT...","description":"Sequence of an adapter ligated to the 3' end."},{"names":["--p-front"],"argument":"TEXT...","description":"Sequence of an adapter ligated to the 5' end."},{"names":["--p-anywhere"],"argument":"TEXT...","description":"Sequence of an adapter that may be ligated to the 5' or 3' end."},{"names":["--p-error-rate"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"Maximum allowed error rate. [default: 0.1]"},{"names":["--p-indels","--p-no-indels"],"argument":"","description":"Allow insertions or deletions of bases when matching adapters."},{"names":["--p-times"],"argument":"INTEGER","description":"Remove multiple occurrences of an adapter if it is repeated, up to `times` times."},{"names":["--p-overlap"],"argument":"INTEGER","description":"Require at least `overlap` bases of overlap between read and adapter for an adapter to be found."},{"names":["--p-match-read-wildcards","--p-no-match-read-wildcards"],"argument":"","description":"Interpret IUPAC wildcards (e.g., N) in reads."},{"names":["--p-match-adapter-wildcards","--p-no-match-adapter-wildcards"],"argument":"","description":"Interpret IUPAC wildcards (e.g., N) in adapters."},{"names":["--p-minimum-length"],"argument":"INTEGER","description":"Discard reads shorter than specified value."},{"names":["--p-discard-untrimmed","--p-no-discard-untrimmed"],"argument":"","description":"Discard reads in which no adapter was found."},{"names":["--p-max-expected-errors"],"argument":"NUMBER","description":"Discard reads that exceed maximum expected erroneous nucleotides."},{"names":["--p-max-n"],"argument":"NUMBER","description":"Discard reads with more than COUNT N bases."},{"names":["--p-quality-cutoff-5end"],"argument":"INTEGER","description":"Trim nucleotides with Phred score quality lower than threshold from 5 prime end."},{"names":["--p-quality-cutoff-3end"],"argument":"INTEGER","description":"Trim nucleotides with Phred score quality lower than threshold from 3 prime end."},{"names":["--p-quality-base"],"argument":"INTEGER","description":"How the Phred score is encoded (33 or 64)."},{"names":["--o-trimmed-sequences"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The resulting trimmed sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"dada2","description":"Plugin for sequence quality control with DADA2.","usage":"qiime dada2 [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"denoise-ccs","description":"Denoise and dereplicate single-end Pacbio CCS","usage":"qiime dada2 denoise-ccs [OPTIONS]","options":[{"names":["--i-demultiplexed-seqs"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The single-end demultiplexed PacBio CCS sequences to be denoised. [required]"},{"names":["--p-front"],"argument":"TEXT","description":"Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded. Each read is re-oriented if the reverse complement of the read is a better match to the provided primer sequence. This is recommended for PacBio CCS reads, which come in a random mix of forward and reverse-complement orientations. [required]"},{"names":["--p-adapter"],"argument":"TEXT","description":"Sequence of an adapter ligated to the 3' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded. [required]"},{"names":["--p-max-mismatch"],"argument":"INTEGER","description":"The number of mismatches to tolerate when matching reads to primer sequences - see http://benjjneb.github.io/dada2/ for complete details. [default: 2]"},{"names":["--p-indels","--p-no-indels"],"argument":"","description":"Allow insertions or deletions of bases when matching adapters. Note that primer matching can be significantly slower, currently about 4x slower"},{"names":["--p-trunc-len"],"argument":"INTEGER","description":"Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed. Note: Since Pacbio CCS sequences were normally with very high quality scores, there is no need to truncate the Pacbio CCS sequences."},{"names":["--p-trim-left"],"argument":"INTEGER","description":"Position at which sequences should be trimmed due to low quality. This trims the 5' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]"},{"names":["--p-max-ee"],"argument":"NUMBER","description":"Reads with number of expected errors higher than this value will be discarded. [default: 2.0]"},{"names":["--p-trunc-q"],"argument":"INTEGER","description":"Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]"},{"names":["--p-min-len"],"argument":"INTEGER","description":"Remove reads with length less than minLen. minLen is enforced after trimming and truncation. For 16S Pacbio CCS, suggest 1000. [default: 20]"},{"names":["--p-max-len"],"argument":"INTEGER","description":"Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length. For 16S Pacbio CCS, suggest 1600. [default: 0]"},{"names":["--p-pooling-method"],"argument":"TEXT Choices('independent', 'pseudo')","description":"The method used to pool samples for denoising. \"independent\": Samples are denoised indpendently. \"pseudo\": The pseudo-pooling method is used to approximate pooling of samples. 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Smaller numbers will result in a shorter run time but a less reliable error model."},{"names":["--p-hashed-feature-ids","--p-no-hashed-feature-ids"],"argument":"","description":"If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]"},{"names":["--p-retain-all-samples","--p-no-retain-all-samples"],"argument":"","description":"If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table."},{"names":["--o-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting feature table. [required]"},{"names":["--o-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]"},{"names":["--o-denoising-stats"],"argument":"ARTIFACT SampleData[DADA2Stats]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"denoise-paired","description":"Denoise and dereplicate paired-end sequences","usage":"qiime dada2 denoise-paired [OPTIONS]","options":[{"names":["--i-demultiplexed-seqs"],"argument":"ARTIFACT SampleData[PairedEndSequencesWithQuality]","description":"The paired-end demultiplexed sequences to be denoised. [required]"},{"names":["--p-trunc-len-f"],"argument":"INTEGER","description":"Position at which forward read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]"},{"names":["--p-trunc-len-r"],"argument":"INTEGER","description":"Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]"},{"names":["--p-trim-left-f"],"argument":"INTEGER","description":"Position at which forward read sequences should be trimmed due to low quality. 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If the resulting read is then shorter than `trunc-len-f` or `trunc-len-r` (depending on the direction of the read) it is discarded. [default: 2]"},{"names":["--p-min-overlap"],"argument":"INTEGER","description":"The minimum length of the overlap required for merging the forward and reverse reads."},{"names":["--p-pooling-method"],"argument":"TEXT Choices('independent', 'pseudo')","description":"The method used to pool samples for denoising. \"independent\": Samples are denoised indpendently. \"pseudo\": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs."},{"names":["--p-chimera-method"],"argument":"TEXT Choices('consensus', 'none', 'pooled')","description":"The method used to remove chimeras. \"none\": No chimera removal is performed. \"pooled\": All reads are pooled prior to chimera detection. \"consensus\": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: 'consensus']"},{"names":["--p-min-fold-parent-over-abundance"],"argument":"NUMBER","description":"The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. 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[required]"},{"names":["--o-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence, and these sequences will be the joined paired-end sequences. [required]"},{"names":["--o-denoising-stats"],"argument":"ARTIFACT SampleData[DADA2Stats]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"denoise-pyro","description":"Denoise and dereplicate single-end pyrosequences","usage":"qiime dada2 denoise-pyro [OPTIONS]","options":[{"names":["--i-demultiplexed-seqs"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The single-end demultiplexed pyrosequencing sequences (e.g. 454, IonTorrent) to be denoised."},{"names":["--p-trunc-len"],"argument":"INTEGER","description":"Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed [required]"},{"names":["--p-trim-left"],"argument":"INTEGER","description":"Position at which sequences should be trimmed due to low quality. This trims the 5' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]"},{"names":["--p-max-ee"],"argument":"NUMBER","description":"Reads with number of expected errors higher than this value will be discarded. [default: 2.0]"},{"names":["--p-trunc-q"],"argument":"INTEGER","description":"Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]"},{"names":["--p-max-len"],"argument":"INTEGER","description":"Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length. [default: 0]"},{"names":["--p-pooling-method"],"argument":"TEXT Choices('independent', 'pseudo')","description":"The method used to pool samples for denoising. \"independent\": Samples are denoised independently. \"pseudo\": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs."},{"names":["--p-chimera-method"],"argument":"TEXT Choices('consensus', 'none', 'pooled')","description":"The method used to remove chimeras. \"none\": No chimera removal is performed. \"pooled\": All reads are pooled prior to chimera detection. \"consensus\": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. 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[default: 1]"},{"names":["--p-n-reads-learn"],"argument":"INTEGER","description":"The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model."},{"names":["--p-hashed-feature-ids","--p-no-hashed-feature-ids"],"argument":"","description":"If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. 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Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"denoise-single","description":"Denoise and dereplicate single-end sequences","usage":"qiime dada2 denoise-single [OPTIONS]","options":[{"names":["--p-trunc-len"],"argument":"INTEGER","description":"Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed [required]"},{"names":["--p-trim-left"],"argument":"INTEGER","description":"Position at which sequences should be trimmed due to low quality. 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In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs."},{"names":["--p-chimera-method"],"argument":"TEXT Choices('consensus', 'none', 'pooled')","description":"The method used to remove chimeras. \"none\": No chimera removal is performed. \"pooled\": All reads are pooled prior to chimera detection. \"consensus\": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: 'consensus']"},{"names":["--p-min-fold-parent-over-abundance"],"argument":"NUMBER","description":"The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is \"none\". [default: 1.0]"},{"names":["--p-allow-one-off","--p-no-allow-one-off"],"argument":"","description":"Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is True.If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera. [default: False]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]"},{"names":["--p-n-reads-learn"],"argument":"INTEGER","description":"The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model."},{"names":["--p-hashed-feature-ids","--p-no-hashed-feature-ids"],"argument":"","description":"If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]"},{"names":["--p-retain-all-samples","--p-no-retain-all-samples"],"argument":"","description":"If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table."},{"names":["--o-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting feature table. [required]"},{"names":["--o-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]"},{"names":["--o-denoising-stats"],"argument":"ARTIFACT SampleData[DADA2Stats]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"deblur","description":"Plugin for sequence quality control with Deblur.","usage":"qiime deblur [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"denoise-16S","description":"Deblur sequences using a 16S positive filter.","usage":"qiime deblur denoise-16S [OPTIONS]","options":[{"names":["--p-trim-length"],"argument":"INTEGER","description":"Sequence trim length, specify -1 to disable trimming. [required]"},{"names":["--p-sample-stats","--p-no-sample-stats"],"argument":"","description":"If true, gather stats per sample. [default: False]"},{"names":["--p-mean-error"],"argument":"NUMBER","description":"The mean per nucleotide error, used for original sequence estimate. [default: 0.005]"},{"names":["--p-indel-prob"],"argument":"NUMBER","description":"Insertion/deletion (indel) probability (same for N indels). [default: 0.01]"},{"names":["--p-indel-max"],"argument":"INTEGER","description":"Maximum number of insertion/deletions. [default: 3]"},{"names":["--p-min-reads"],"argument":"INTEGER","description":"Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]"},{"names":["--p-min-size"],"argument":"INTEGER","description":"In each sample, discard all features with an abundance less than min-size. 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[required]"},{"names":["--o-stats"],"argument":"ARTIFACT","description":"Per-sample stats if requested."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. 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[required]"},{"names":["--p-sample-stats","--p-no-sample-stats"],"argument":"","description":"If true, gather stats per sample. [default: False]"},{"names":["--p-mean-error"],"argument":"NUMBER","description":"The mean per nucleotide error, used for original sequence estimate. [default: 0.005]"},{"names":["--p-indel-prob"],"argument":"NUMBER","description":"Insertion/deletion (indel) probability (same for N indels). [default: 0.01]"},{"names":["--p-indel-max"],"argument":"INTEGER","description":"Maximum number of insertion/deletions. [default: 3]"},{"names":["--p-min-reads"],"argument":"INTEGER","description":"Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]"},{"names":["--p-min-size"],"argument":"INTEGER","description":"In each sample, discard all features with an abundance less than min-size. [default: 2]"},{"names":["--p-jobs-to-start"],"argument":"NTHREADS","description":"Number of jobs to start (if to run in parallel)."},{"names":["--p-hashed-feature-ids","--p-no-hashed-feature-ids"],"argument":"","description":"If true, hash the feature IDs. [default: True]"},{"names":["--p-left-trim-len"],"argument":"INTEGER","description":"Sequence trimming from the 5' end. A value of 0 will"},{"names":["--o-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting denoised feature table. [required]"},{"names":["--o-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting feature sequences. [required]"},{"names":["--o-stats"],"argument":"ARTIFACT","description":"Per-sample stats if requested. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"visualize-stats","description":"Visualize Deblur stats per sample.","usage":"qiime deblur visualize-stats [OPTIONS]","options":[{"names":["--i-deblur-stats"],"argument":"ARTIFACT","description":"DeblurStats Summary statistics of the Deblur process. [required]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"demux","description":"Plugin for demultiplexing & viewing sequence quality.","usage":"qiime demux [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"emp-paired","description":"Demultiplex paired-end sequence data generated with the EMP protocol.","usage":"qiime demux emp-paired [OPTIONS]","options":[{"names":["--i-seqs"],"argument":"ARTIFACT EMPPairedEndSequences","description":"The paired-end sequences to be demultiplexed."},{"names":["--m-barcodes-file","--m-barcodes-column"],"argument":"METADATA","description":"The sample metadata column containing the per-sample barcodes. [required]"},{"names":["--p-golay-error-correction","--p-no-golay-error-correction"],"argument":"","description":"Perform 12nt Golay error correction on the barcode reads. [default: True]"},{"names":["--p-rev-comp-barcodes","--p-no-rev-comp-barcodes"],"argument":"","description":"If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing."},{"names":["--p-rev-comp-mapping-barcodes","--p-no-rev-comp-mapping-barcodes"],"argument":"","description":"If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]"},{"names":["--p-ignore-description-mismatch","--p-no-ignore-description-mismatch"],"argument":"","description":"If enabled, ignore mismatches in sequence record description fields. [default: False]"},{"names":["--o-error-correction-details"],"argument":"ARTIFACT ErrorCorrectionDetails","description":"Detail about the barcode error corrections. [required]"},{"names":["--o-per-sample-sequences"],"argument":"ARTIFACT","description":"SampleData[PairedEndSequencesWithQuality]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. 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[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-samples","description":"Filter samples out of demultiplexed data.","usage":"qiime demux filter-samples [OPTIONS]","options":[{"names":["--i-demux"],"argument":"ARTIFACT","description":"The demultiplexed data from which samples should be filtered. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata indicating which sample ids to filter. [required]"},{"names":["--p-where"],"argument":"TEXT","description":"Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. 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[required]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the demultiplexed"},{"names":["--o-partitioned-demux"],"argument":"ARTIFACTS...","description":"Collection[SampleData[PairedEndSequencesWithQuality]]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partition-samples-single","description":"Split demultiplexed sequence data into partitions.","usage":"qiime demux partition-samples-single [OPTIONS]","options":[{"names":["--i-demux"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The demultiplexed sequences to partition. [required]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the demultiplexed"},{"names":["--o-partitioned-demux"],"argument":"ARTIFACTS...","description":"Collection[SampleData[SequencesWithQuality]]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. 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Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"subsample-single","description":"Subsample single-end sequences without replacement.","usage":"qiime demux subsample-single [OPTIONS]","options":[{"names":["--p-fraction"],"argument":"PROPORTION Range(0, 1, inclusive_start=False)","description":"The fraction of sequences to retain in subsample."},{"names":["--o-subsampled-sequences"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"The subsampled sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"summarize","description":"Summarize counts per sample.","usage":"qiime demux summarize [OPTIONS]","options":[{"names":["--p-n"],"argument":"INTEGER","description":"The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tabulate-read-counts","description":"Tabulate counts per sample","usage":"qiime demux tabulate-read-counts [OPTIONS]","options":[{"names":["--o-counts"],"argument":"ARTIFACT","description":"ImmutableMetadata [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"diversity","description":"Plugin for exploring community diversity.","usage":"qiime diversity [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"adonis","description":"adonis PERMANOVA test for beta group significance","usage":"qiime diversity adonis [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata containing formula terms. [required]"},{"names":["--p-formula"],"argument":"TEXT","description":"Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula \"treatment+block\" would test whether the input distance matrix partitions based on \"treatment\" and \"block\" sample metadata. The formula \"treatment*block\" would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of parallel processes to run"},{"names":["--p-permutations"],"argument":"INTEGER","description":"The number of permutations to be run when computing"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"alpha","description":"Alpha diversity","usage":"qiime diversity alpha [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The feature table containing the samples for which"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence","description":"The feature table containing the samples for which"},{"names":["--o-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample alpha diversities."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"alpha-correlation","description":"Alpha diversity correlation","usage":"qiime diversity alpha-correlation [OPTIONS]","options":[{"names":["--i-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of alpha diversity values by sample. 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[required]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"alpha-phylogenetic","description":"Alpha diversity (phylogenetic)","usage":"qiime diversity alpha-phylogenetic [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]","description":"The feature table containing the samples for which alpha diversity should be computed. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"The alpha diversity metric to be computed. [required]"},{"names":["--o-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample alpha diversities. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"alpha-rarefaction","description":"Alpha rarefaction curves","usage":"qiime diversity alpha-rarefaction [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table to compute rarefaction curves from. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Optional phylogeny for phylogenetic metrics."},{"names":["--p-max-depth"],"argument":"INTEGER","description":"The maximum rarefaction depth. Must be greater than min-depth. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata."},{"names":["--p-min-depth"],"argument":"INTEGER","description":"The minimum rarefaction depth."},{"names":["--p-steps"],"argument":"INTEGER","description":"The number of rarefaction depths to include between min-depth and max-depth. [default: 10]"},{"names":["--p-iterations"],"argument":"INTEGER","description":"The number of rarefied feature tables to compute at each step. [default: 10]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta","description":"Beta diversity","usage":"qiime diversity beta [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]","description":"The feature table containing the samples over which beta diversity should be computed. [required]"},{"names":["--p-metric"],"argument":"{aitchison, braycurtis, canberra, canberra_adkins, chebyshev, cityblock, correlation, cosine, dice, euclidean, hamming, jaccard, jensenshannon, kulsinski, matching, minkowski, rogerstanimoto, russellrao, seuclidean, sokalmichener, sokalsneath, sqeuclidean, yule}","description":"The beta diversity metric to be computed."},{"names":["--p-pseudocount"],"argument":"INTEGER","description":"A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = 'auto', one job will be launched for each identified CPU core on the host. [default: 1]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix The resulting distance matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-correlation","description":"Beta diversity correlation","usage":"qiime diversity beta-correlation [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Numeric metadata column from which to compute pairwise Euclidean distances [required]"},{"names":["--p-method"],"argument":"TEXT Choices('spearman', 'pearson')","description":"The correlation test to be applied in the Mantel test. [default: 'spearman']"},{"names":["--p-permutations"],"argument":"INTEGER","description":"The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]"},{"names":["--p-intersect-ids","--p-no-intersect-ids"],"argument":"","description":"If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]"},{"names":["--p-label1"],"argument":"TEXT","description":"Label for `distance-matrix` in the output visualization. [default: 'Distance Matrix']"},{"names":["--p-label2"],"argument":"TEXT","description":"Label for `metadata-distance-matrix` in the output visualization. [default: 'Metadata']"},{"names":["--p-permutations"],"argument":"INTEGER","description":"The number of permutations to be run when computing p-values."},{"names":["--o-metadata-distance-matrix"],"argument":"ARTIFACT","description":"The Distance Matrix produced from the metadata column and used in the mantel test [required]"},{"names":["--o-mantel-scatter-visualization"],"argument":"VISUALIZATION","description":"Scatter plot rendering of the manteltest results [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-group-significance","description":"Beta diversity group significance","usage":"qiime diversity beta-group-significance [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples."},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Categorical sample metadata column. [required]"},{"names":["--p-method"],"argument":"TEXT Choices('permanova', 'anosim', 'permdisp')","description":"The group significance test to be applied."},{"names":["--p-pairwise","--p-no-pairwise"],"argument":"","description":"Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column. [default: False]"},{"names":["--p-permutations"],"argument":"INTEGER","description":"The number of permutations to be run when computing p-values. [default: 999]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-phylogenetic","description":"Beta diversity (phylogenetic)","usage":"qiime diversity beta-phylogenetic [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]","description":"The feature table containing the samples over which beta diversity should be computed. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]"},{"names":["--p-metric"],"argument":"{generalized_unifrac, unweighted_unifrac, weighted_normalized_unifrac, weighted_unifrac}","description":"The beta diversity metric to be computed. [required]"},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."},{"names":["--p-variance-adjusted","--p-no-variance-adjusted"],"argument":"","description":"Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]"},{"names":["--p-alpha"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"This parameter is only used when the choice of metric is generalized_unifrac. 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Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-rarefaction","description":"Beta diversity rarefaction","usage":"qiime diversity beta-rarefaction [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table upon which to perform beta diversity rarefaction analyses. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required for phylogenetic metrics] [optional]"},{"names":["--p-metric"],"argument":"{aitchison, braycurtis, canberra, canberra_adkins, chebyshev, cityblock, correlation, cosine, dice, euclidean, generalized_unifrac, hamming, jaccard, jensenshannon, kulsinski, matching, minkowski, rogerstanimoto, russellrao, seuclidean, sokalmichener, sokalsneath, sqeuclidean, unweighted_unifrac, weighted_normalized_unifrac, weighted_unifrac, yule}","description":"The beta diversity metric to be computed. [required]"},{"names":["--p-clustering-method"],"argument":"{nj, upgma}","description":"Samples can be clustered with neighbor joining or UPGMA. An arbitrary rarefaction trial will be used for the tree, and the remaining trials are used to calculate the support of the internal nodes of that tree. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata used for the Emperor jackknifed PCoA plot. [required]"},{"names":["--p-sampling-depth"],"argument":"INTEGER","description":"The total frequency that each sample should be rarefied to prior to computing the diversity metric. [required]"},{"names":["--p-iterations"],"argument":"INTEGER","description":"Number of times to rarefy the feature table at a given sampling depth. [default: 10]"},{"names":["--p-clustering-method"],"argument":"TEXT Choices('nj', 'upgma')","description":"Samples can be clustered with neighbor joining or UPGMA. An arbitrary rarefaction trial will be used for the tree, and the remaining trials are used to calculate the support of the internal nodes of that tree. [required]"},{"names":["--p-correlation-method"],"argument":"TEXT Choices('pearson', 'spearman')","description":"The Mantel correlation test to be applied when computing correlation between beta diversity distance matrices. [default: 'spearman']"},{"names":["--p-color-scheme"],"argument":"{BrBG, BrBG_r, PRGn, PRGn_r, PiYG, PiYG_r, PuOr, PuOr_r, RdBu, RdBu_r, RdGy, RdGy_r, RdYlBu, RdYlBu_r, RdYlGn, RdYlGn_r}","description":"The matplotlib color scheme to generate the heatmap with."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"bioenv","description":"bioenv","usage":"qiime diversity bioenv [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples."},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"core-metrics","description":"Core diversity metrics (non-phylogenetic)","usage":"qiime diversity core-metrics [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table containing the samples over which diversity metrics should be computed. [required]"},{"names":["--p-sampling-depth"],"argument":"INTEGER","description":"The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata to use in the emperor plots. [required]"},{"names":["--p-with-replacement","--p-no-with-replacement"],"argument":"","description":"Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"[beta methods only] - The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = 'auto', one job will be launched for each identified CPU core on the host. [default: 1]"},{"names":["--p-ignore-missing-samples","--p-no-ignore-missing-samples"],"argument":"","description":"If set to `True` samples and features without metadata are included by setting all metadata values to: \"This element has no metadata\". By default an exception will be raised if missing elements are encountered. Note, this flag only takes effect if there is at least one overlapping element."},{"names":["--o-rarefied-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting rarefied feature table. [required]"},{"names":["--o-observed-features-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Observed Features values by sample. [required]"},{"names":["--o-shannon-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Shannon diversity values by sample. [required]"},{"names":["--o-evenness-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Pielou's evenness values by sample. [required]"},{"names":["--o-jaccard-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of Jaccard distances between pairs of samples. [required]"},{"names":["--o-bray-curtis-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of Bray-Curtis distances between pairs of samples. [required]"},{"names":["--o-jaccard-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from Jaccard distances between samples. [required]"},{"names":["--o-bray-curtis-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from Bray-Curtis distances Bray-Curtis. [required]"},{"names":["--o-jaccard-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from Jaccard. [required]"},{"names":["--o-bray-curtis-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from Bray-Curtis. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"core-metrics-phylogenetic","description":"Core diversity metrics (phylogenetic and non-phylogenetic)","usage":"qiime diversity core-metrics-phylogenetic [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table containing the samples over which diversity metrics should be computed. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]"},{"names":["--p-sampling-depth"],"argument":"INTEGER","description":"The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata to use in the emperor plots. [required]"},{"names":["--p-with-replacement","--p-no-with-replacement"],"argument":"","description":"Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]"},{"names":["--o-rarefied-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting rarefied feature table. [required]"},{"names":["--o-faith-pd-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Faith PD values by sample. [required]"},{"names":["--o-observed-features-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Observed Features values by sample. [required]"},{"names":["--o-shannon-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Shannon diversity values by sample. [required]"},{"names":["--o-evenness-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector of Pielou's evenness values by sample. [required]"},{"names":["--o-unweighted-unifrac-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of unweighted UniFrac distances between pairs of samples. [required]"},{"names":["--o-weighted-unifrac-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of weighted UniFrac distances between pairs of samples. [required]"},{"names":["--o-jaccard-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of Jaccard distances between pairs of samples. [required]"},{"names":["--o-bray-curtis-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of Bray-Curtis distances between pairs of samples. [required]"},{"names":["--o-unweighted-unifrac-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from unweighted UniFrac distances between samples. [required]"},{"names":["--o-weighted-unifrac-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from weighted UniFrac distances between samples. [required]"},{"names":["--o-jaccard-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from Jaccard distances between samples. [required]"},{"names":["--o-bray-curtis-pcoa-results"],"argument":"ARTIFACT","description":"PCoA matrix computed from Bray-Curtis distances samples. [required]"},{"names":["--o-unweighted-unifrac-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from unweighted UniFrac. [required]"},{"names":["--o-weighted-unifrac-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from weighted UniFrac. [required]"},{"names":["--o-jaccard-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from Jaccard. [required]"},{"names":["--o-bray-curtis-emperor"],"argument":"VISUALIZATION","description":"Emperor plot of the PCoA matrix computed from Bray-Curtis. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-alpha-diversity","description":"Filter samples from an alpha diversity metric.","usage":"qiime diversity filter-alpha-diversity [OPTIONS]","options":[{"names":["--i-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Alpha diversity sample data to filter by sample. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata used to select samples to retain from the sample data (default) or select samples to exclude using the `exclude-ids` parameter. [required]"},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered alpha diversity artifact. If not provided, all samples in `metadata` that are also in the input alpha diversity artifact will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"If `True`, the samples selected by `metadata` or the `where` parameters will be excluded from the filtered alpha diversity artifact instead of being retained."},{"names":["--o-filtered-alpha-diversity"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-distance-matrix","description":"Filter samples from a distance matrix.","usage":"qiime diversity filter-distance-matrix [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix to filter by sample. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude-ids` when selecting samples to discard. [required]"},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained."},{"names":["--o-filtered-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix filtered to include samples matching"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"mantel","description":"Apply the Mantel test to two distance matrices","usage":"qiime diversity mantel [OPTIONS]","options":[{"names":["--i-dm1"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--i-dm2"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--p-method"],"argument":"{spearman, pearson}","description":"The correlation test to be applied in the Mantel test."},{"names":["--p-permutations"],"argument":"INTEGER","description":"The number of permutations to be run when computing p-values."},{"names":["--p-intersect-ids","--p-no-intersect-ids"],"argument":"","description":"If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]"},{"names":["--p-label1"],"argument":"TEXT","description":"Label for `dm1` in the output visualization."},{"names":["--p-label2"],"argument":"TEXT","description":"Label for `dm2` in the output visualization."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partial-procrustes","description":"Partial Procrustes","usage":"qiime diversity partial-procrustes [OPTIONS]","options":[{"names":["--i-reference"],"argument":"ARTIFACT","description":"The ordination matrix to which data is fitted to. [required]"},{"names":["--i-other"],"argument":"ARTIFACT","description":"The ordination matrix that's fitted to the reference ordination. [required]"},{"names":["--m-pairing-file"],"argument":"METADATA","description":"The metadata file."},{"names":["--m-pairing-column"],"argument":"COLUMN","description":"The metadata column describing sample pairs which exist. [required]"},{"names":["--p-dimensions"],"argument":"INTEGER","description":"The number of dimensions to use when fitting the two matrices of the reference ordination. [required]"},{"names":["--o-transformed"],"argument":"ARTIFACT","description":"The 'other' ordination transformed into the space of the reference ordination. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"pcoa","description":"Principal Coordinate Analysis","usage":"qiime diversity pcoa [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"The distance matrix on which PCoA should be computed. [required]"},{"names":["--p-number-of-dimensions"],"argument":"INTEGER","description":"Dimensions to reduce the distance matrix to. This number determines how many eigenvectors and eigenvalues are returned,and influences the choice of algorithm used to compute them. By default, uses the default eigendecomposition method, SciPy's eigh, which computes all eigenvectors and eigenvalues in an exact manner. For very large matrices, this is expected to be slow. If a value is specified for this parameter, then the fast, heuristic eigendecomposition algorithm fsvd is used, which only computes and returns the number of dimensions specified, but suffers some degree of accuracy loss, the magnitude of which varies across different datasets. [optional]"},{"names":["--o-pcoa"],"argument":"ARTIFACT","description":"The resulting PCoA matrix."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"pcoa-biplot","description":"Principal Coordinate Analysis Biplot","usage":"qiime diversity pcoa-biplot [OPTIONS]","options":[{"names":["--i-pcoa"],"argument":"ARTIFACT","description":"The PCoA where the features will be projected onto."},{"names":["--i-features"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Variables to project onto the PCoA matrix [required]"},{"names":["--o-biplot"],"argument":"ARTIFACT","description":"The resulting PCoA matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"procrustes-analysis","description":"Procrustes Analysis","usage":"qiime diversity procrustes-analysis [OPTIONS]","options":[{"names":["--i-reference"],"argument":"ARTIFACT","description":"The ordination matrix to which data is fitted to. [required]"},{"names":["--i-other"],"argument":"ARTIFACT","description":"The ordination matrix that's fitted to the reference ordination. [required]"},{"names":["--p-dimensions"],"argument":"INTEGER","description":"The number of dimensions to use when fitting the two matrices [default: 5]"},{"names":["--p-permutations"],"argument":"VALUE","description":"The number of permutations to be run when computing p-values. Supplying a value of `disable` will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]"},{"names":["--o-transformed-reference"],"argument":"ARTIFACT","description":"A normalized version of the \"reference\" ordination matrix. [required]"},{"names":["--o-transformed-other"],"argument":"ARTIFACT","description":"A normalized and fitted version of the \"other\" ordination matrix. [required]"},{"names":["--o-disparity-results"],"argument":"ARTIFACT","description":"The sum of the squares of the pointwise differences between the two input datasets & its p value. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tsne","description":"t-distributed stochastic neighbor embedding","usage":"qiime diversity tsne [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"The distance matrix on which t-SNE should be computed. [required]"},{"names":["--p-number-of-dimensions"],"argument":"INTEGER","description":"Dimensions to reduce the distance matrix to. [required]"},{"names":["--p-perplexity"],"argument":"NUMBER","description":"Provide the balance between local and global structure. Low values concentrate on local structure. [default: 25.0]"},{"names":["--p-n-iter"],"argument":"INTEGER","description":"[default: 1000]"},{"names":["--p-learning-rate"],"argument":"NUMBER","description":"Controls how much the weights are adjusted at each update. [default: 200.0]"},{"names":["--p-early-exaggeration"],"argument":"NUMBER","description":"Affects the tightness of the shown clusters. Larger values increase the distance between natural clusters in the embedded space. [default: 12.0]"},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--o-tsne"],"argument":"ARTIFACT","description":"The resulting t-SNE matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"umap","description":"Uniform Manifold Approximation and Projection","usage":"qiime diversity umap [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"The distance matrix on which UMAP should be computed. [required]"},{"names":["--p-number-of-dimensions"],"argument":"INTEGER","description":"Dimensions to reduce the distance matrix to."},{"names":["--p-n-neighbors"],"argument":"INTEGER","description":"Provide the balance between local and global structure."},{"names":["--p-min-dist"],"argument":"NUMBER","description":"Controls the cluster size. Low values cause clumpier clusters."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--o-umap"],"argument":"ARTIFACT","description":"The resulting UMAP matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"diversity-lib","description":"Plugin for computing community diversity.","usage":"qiime diversity-lib [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"alpha-passthrough","description":"Alpha Passthrough (non-phylogenetic)","usage":"qiime diversity-lib alpha-passthrough [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table containing the samples for which a selected metric should be computed. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"The alpha diversity metric to be computed. [required]"},{"names":["--o-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample values for the chosen metric. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-passthrough","description":"Beta Passthrough (non-phylogenetic)","usage":"qiime diversity-lib beta-passthrough [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table containing the samples over which beta diversity should be computed. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"The beta diversity metric to be computed. [required]"},{"names":["--p-pseudocount"],"argument":"INTEGER","description":"A pseudocount to handle zeros for compositional metrics."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = 'auto', one job will be launched for each identified CPU core on the host. [default: 1]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix The resulting distance matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"beta-phylogenetic-passthrough","description":"Beta Phylogenetic Passthrough","usage":"qiime diversity-lib beta-phylogenetic-passthrough [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table containing the samples over which beta diversity should be computed. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"The beta diversity metric to be computed. [required]"},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."},{"names":["--p-variance-adjusted","--p-no-variance-adjusted"],"argument":"","description":"Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]"},{"names":["--p-alpha"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized. [optional]"},{"names":["--p-bypass-tips","--p-no-bypass-tips"],"argument":"","description":"In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix The resulting distance matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"bray-curtis","description":"Bray-Curtis Dissimilarity","usage":"qiime diversity-lib bray-curtis [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency]","description":"The feature table containing the samples for which Bray-Curtis dissimilarity should be computed."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = 'auto', one job will be launched for each identified CPU core on the host. [default: 1]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix for Bray-Curtis dissimilarity"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."},{"names":["--o-distance-matrix"],"argument":"bray-curtis-dm.qza","description":"# ### example: use 'auto' to run on all of host system's available CPU cores"}]},{"name":"faith-pd","description":"Faith's Phylogenetic Diversity","usage":"qiime diversity-lib faith-pd [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The feature table containing the samples for which"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence","description":"The feature table containing the samples for which"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that   Phylogeny[Rooted] correspond to the feature identifiers in the table."},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."},{"names":["--o-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample values for Faith's Phylogenetic Diversity. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"jaccard","description":"Jaccard Distance","usage":"qiime diversity-lib jaccard [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The feature table containing the samples for which"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence","description":"The feature table containing the samples for which"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = 'auto', one job will be launched for each identified CPU core on the host. [default: 1]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix for Jaccard index [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."},{"names":["--o-distance-matrix"],"argument":"jaccard-dm.qza","description":"# ### example: use 'auto' to run on all of host system's available CPU cores"}]},{"name":"observed-features","description":"Observed Features","usage":"qiime diversity-lib observed-features [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The feature table containing the samples for which the"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence","description":"The feature table containing the samples for which the"},{"names":["--o-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample counts of observed features. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"pielou-evenness","description":"Pielou's Evenness","usage":"qiime diversity-lib pielou-evenness [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency]","description":"The feature table containing the samples for which Pielou's evenness should be computed. [required]"},{"names":["--p-drop-undefined-samples","--p-no-drop-undefined-samples"],"argument":"","description":"Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector. [default: False]"},{"names":["--o-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample values for Pielou's Evenness. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"shannon-entropy","description":"Shannon's Entropy","usage":"qiime diversity-lib shannon-entropy [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency]","description":"The feature table containing the samples for which Shannon's Entropy should be computed. [required]"},{"names":["--p-drop-undefined-samples","--p-no-drop-undefined-samples"],"argument":"","description":"Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector. [default: False]"},{"names":["--o-vector"],"argument":"ARTIFACT SampleData[AlphaDiversity]","description":"Vector containing per-sample values for Shannon's Entropy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"unweighted-unifrac","description":"Unweighted Unifrac","usage":"qiime diversity-lib unweighted-unifrac [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The feature table containing the samples for which"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence","description":"The feature table containing the samples for which"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that   Phylogeny[Rooted] correspond to the feature identifiers in the table."},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."},{"names":["--p-bypass-tips","--p-no-bypass-tips"],"argument":"","description":"In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix for Unweighted Unifrac. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."},{"names":["--o-distance-matrix"],"argument":"unweighted-unifrac-dm.qza","description":"# ### example: to run on n cores, replace 1 here with your preferred integer"}]},{"name":"weighted-unifrac","description":"Weighted Unifrac","usage":"qiime diversity-lib weighted-unifrac [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency]","description":"The feature table containing the samples for which Weighted Unifrac should be computed. [required]"},{"names":["--i-phylogeny"],"argument":"ARTIFACT","description":"Phylogenetic tree containing tip identifiers that"},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."},{"names":["--p-bypass-tips","--p-no-bypass-tips"],"argument":"","description":"In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"Distance matrix for Unweighted Unifrac. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."},{"names":["--o-distance-matrix"],"argument":"weighted-unifrac-dm.qza","description":"# ### example: to run on n cores, replace 1 here with your preferred integer"}]}]},{"name":"emperor","description":"Plugin for ordination plotting with Emperor.","usage":"qiime emperor [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"biplot","description":"Visualize and Interact with Principal Coordinates Analysis","usage":"qiime emperor biplot [OPTIONS]","options":[{"names":["--i-biplot"],"argument":"ARTIFACT","description":"The principal coordinates matrix to be plotted. [required]"},{"names":["--m-sample-metadata-file"],"argument":"METADATA...","description":"The sample metadata [required]"},{"names":["--m-feature-metadata-file"],"argument":"METADATA...","description":"The feature metadata (useful to manipulate the arrows in the plot)."},{"names":["--p-ignore-missing-samples","--p-no-ignore-missing-samples"],"argument":"","description":"This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \"This sample has no metadata\". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]"},{"names":["--p-invert","--p-no-invert"],"argument":"","description":"If specified, the point and arrow coordinates will be swapped. [default: False]"},{"names":["--p-number-of-features"],"argument":"","description":"INTEGER"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"plot","description":"Visualize and Interact with Principal Coordinates Analysis","usage":"qiime emperor plot [OPTIONS]","options":[{"names":["--i-pcoa"],"argument":"ARTIFACT","description":"The principal coordinates matrix to be plotted. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata. [required]"},{"names":["--p-ignore-missing-samples","--p-no-ignore-missing-samples"],"argument":"","description":"This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \"This sample has no metadata\". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]"},{"names":["--p-ignore-pcoa-features","--p-no-ignore-pcoa-features"],"argument":"","description":"Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the `biplot` method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised. [default: False]"},{"names":["--p-custom-axes"],"argument":"TEXT...","description":"Numeric sample metadata columns that should be included as axes in the Emperor plot."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"procrustes-plot","description":"Visualize and Interact with a procrustes plot","usage":"qiime emperor procrustes-plot [OPTIONS]","options":[{"names":["--i-reference-pcoa"],"argument":"ARTIFACT","description":"The reference ordination matrix to be plotted. [required]"},{"names":["--i-other-pcoa"],"argument":"ARTIFACT","description":"The \"other\" ordination matrix to be plotted (the one that was fitted to the reference). [required]"},{"names":["--i-m2-stats"],"argument":"ARTIFACT ProcrustesStatistics","description":"The M^2 value of the procrustes analysis & its associated p value. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata. [required]"},{"names":["--p-custom-axes"],"argument":"TEXT...","description":"Numeric sample metadata columns that should be included as axes in the Emperor plot."},{"names":["--p-ignore-missing-samples","--p-no-ignore-missing-samples"],"argument":"","description":"This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \"This sample has no metadata\". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"feature-classifier","description":"Plugin for taxonomic classification.","usage":"qiime feature-classifier [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"blast","description":"BLAST+ local alignment search.","usage":"qiime feature-classifier blast [OPTIONS]","options":[{"names":["--i-query"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query sequences. [required]"},{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences. Incompatible with blastdb."},{"names":["--i-blastdb"],"argument":"ARTIFACT","description":"BLAST indexed database. Incompatible with"},{"names":["--p-maxaccepts"],"argument":"INTEGER","description":"Maximum number of hits to keep for each query."},{"names":["--p-perc-identity"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if percent identity to query is lower."},{"names":["--p-query-cov"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. [default: 0.8]"},{"names":["--p-strand"],"argument":"TEXT Choices('both', 'plus', 'minus')","description":"Align against reference sequences in forward (\"plus\"), reverse (\"minus\"), or both directions (\"both\"). [default: 'both']"},{"names":["--p-evalue"],"argument":"NUMBER","description":"BLAST expectation value (E) threshold for saving hits. [default: 0.001]"},{"names":["--p-output-no-hits","--p-no-output-no-hits"],"argument":"","description":"Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. Set to FALSE to mirror default BLAST search."},{"names":["--p-num-threads"],"argument":"NTHREADS","description":"Number of threads (CPUs) to use in the BLAST search. Pass 0 to use all available CPUs."},{"names":["--o-search-results"],"argument":"ARTIFACT","description":"FeatureData[BLAST6] Top hits for each query. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-consensus-blast","description":"BLAST+ consensus taxonomy classifier","usage":"qiime feature-classifier classify-consensus-blast [OPTIONS]","options":[{"names":["--i-query"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query sequences. [required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"reference taxonomy labels. [required]"},{"names":["--i-blastdb"],"argument":"ARTIFACT","description":"BLAST indexed database. Incompatible with"},{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences. Incompatible with blastdb."},{"names":["--p-maxaccepts"],"argument":"INTEGER","description":"Maximum number of hits to keep for each query."},{"names":["--p-perc-identity"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if percent identity to query is lower."},{"names":["--p-query-cov"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. [default: 0.8]"},{"names":["--p-strand"],"argument":"TEXT Choices('both', 'plus', 'minus')","description":"Align against reference sequences in forward (\"plus\"), reverse (\"minus\"), or both directions (\"both\"). [default: 'both']"},{"names":["--p-evalue"],"argument":"NUMBER","description":"BLAST expectation value (E) threshold for saving hits. [default: 0.001]"},{"names":["--p-output-no-hits","--p-no-output-no-hits"],"argument":"","description":"Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. Set to FALSE to mirror default BLAST search."},{"names":["--p-min-consensus"],"argument":"NUMBER","description":"Minimum fraction of assignments must match top hit to be accepted as consensus assignment."},{"names":["--p-unassignable-label"],"argument":"TEXT","description":"Annotation given to sequences without any hits."},{"names":["--p-num-threads"],"argument":"NTHREADS","description":"Number of threads (CPUs) to use in the BLAST search. Pass 0 to use all available CPUs."},{"names":["--o-classification"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomy classifications of query sequences."},{"names":["--o-search-results"],"argument":"ARTIFACT","description":"FeatureData[BLAST6] Top hits for each query. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-consensus-vsearch","description":"VSEARCH-based consensus taxonomy classifier","usage":"qiime feature-classifier classify-consensus-vsearch [OPTIONS]","options":[{"names":["--i-query"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query Sequences. [required]"},{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences. [required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Reference taxonomy labels. [required]"},{"names":["--p-maxaccepts"],"argument":"VALUE","description":"Maximum number of hits to keep for each query."},{"names":["--p-perc-identity"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if percent identity to query is lower."},{"names":["--p-query-cov"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8]"},{"names":["--p-strand"],"argument":"TEXT Choices('both', 'plus')","description":"Align against reference sequences in forward (\"plus\") or both directions (\"both\")."},{"names":["--p-search-exact","--p-no-search-exact"],"argument":"","description":"Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity, query-cov, maxaccepts, and maxrejects settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False]"},{"names":["--p-top-hits-only","--p-no-top-hits-only"],"argument":"","description":"Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False]"},{"names":["--p-maxhits"],"argument":"VALUE","description":"Maximum number of hits to show once the search is terminated."},{"names":["--p-maxrejects"],"argument":"VALUE","description":"Maximum number of non-matching target sequences to consider before stopping the search."},{"names":["--p-output-no-hits","--p-no-output-no-hits"],"argument":"","description":"Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs."},{"names":["--p-weak-id"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0]"},{"names":["--p-threads"],"argument":"NTHREADS","description":"Number of threads to use for job parallelization. Pass 0 to use one per available CPU. [default: 1]"},{"names":["--p-min-consensus"],"argument":"NUMBER","description":"Minimum fraction of assignments must match top hit to be accepted as consensus assignment."},{"names":["--p-unassignable-label"],"argument":"TEXT","description":"Annotation given to sequences without any hits."},{"names":["--o-classification"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomy classifications of query sequences. [required]"},{"names":["--o-search-results"],"argument":"ARTIFACT","description":"FeatureData[BLAST6] Top hits for each query. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-hybrid-vsearch-sklearn","description":"ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier","usage":"qiime feature-classifier classify-hybrid-vsearch-sklearn","options":[{"names":["--i-query"],"argument":"ARTIFACT","description":"Query Sequences. [required]"},{"names":["--i-reference-reads"],"argument":"ARTIFACT","description":"Reference sequences. [required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT","description":"Reference taxonomy labels. [required]"},{"names":["--i-classifier"],"argument":"ARTIFACT","description":"Pre-trained sklearn taxonomic classifier for classifying the reads. [required]"},{"names":["--p-maxaccepts"],"argument":"VALUE","description":"Maximum number of hits to keep for each query. Set to \"all\" to keep all hits > perc-identity similarity. Note that if strand=both, maxaccepts will keep N hits for each direction (if searches in the opposite direction yield results that exceed the minimum perc-identity). In those cases use maxhits to control the total number of hits returned. This option works in pair with maxrejects. The search process sorts target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if the first target sequence passes the acceptation criteria, it is accepted as best hit and the search process stops for that query. If maxaccepts is set to a higher value, more hits are accepted. If maxaccepts and maxrejects are both set to \"all\", the complete database is searched. [default: 10]"},{"names":["--p-perc-identity"],"argument":"PROPORTION","description":"Percent sequence similarity to use for PREFILTER. Reject match if percent identity to query is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.5]"},{"names":["--p-query-cov"],"argument":"PROPORTION","description":"Query coverage threshold to use for PREFILTER. Reject match if query alignment coverage per high-scoring pair is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.8]"},{"names":["--p-strand"],"argument":"{'both', 'plus'}","description":"Align against reference sequences in forward (\"plus\") or both directions (\"both\"). [default: 'both']"},{"names":["--p-min-consensus"],"argument":"NUMBER","description":"Minimum fraction of assignments must match top hit to be accepted as consensus assignment."},{"names":["--p-maxhits"],"argument":"VALUE","description":"max hits [default: 'all']"},{"names":["--p-maxrejects"],"argument":"VALUE","description":"max rejects [default: 'all']"},{"names":["--p-reads-per-batch"],"argument":"VALUE","description":"Number of reads to process in each batch for sklearn classification. If \"auto\", this parameter is autoscaled to min(number of query sequences / threads, 20000). [default: 'auto']"},{"names":["--p-confidence"],"argument":"VALUE Float","description":"Confidence threshold for limiting taxonomic depth. Set to \"disable\" to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments."},{"names":["--p-read-orientation"],"argument":"{'same', 'reverse-complement', 'auto'}","description":"Direction of reads with respect to reference sequences in pre-trained sklearn classifier. same will cause reads to be classified unchanged; reverse-complement will cause reads to be reversed and complemented prior to classification. \"auto\" will autodetect orientation based on the confidence estimates for the first 100 reads. [default: 'auto']"},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of threads to use for job parallelization. [default: 1]"},{"names":["--p-prefilter","--p-no-prefilter"],"argument":"","description":"Toggle positive filter of query sequences on or off. [default: True]"},{"names":["--p-sample-size"],"argument":"INTEGER","description":"Randomly extract the given number of sequences from the reference database to use for prefiltering. This parameter is ignored if `prefilter` is disabled. [default: 1000]"},{"names":["--p-randseed"],"argument":"INTEGER","description":"Use integer as a seed for the pseudo-random"},{"names":["--o-classification"],"argument":"ARTIFACT","description":"Taxonomy classifications of query sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-sklearn","description":"Pre-fitted sklearn-based taxonomy classifier","usage":"qiime feature-classifier classify-sklearn [OPTIONS]","options":[{"names":["--i-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The feature data to be classified. [required]"},{"names":["--i-classifier"],"argument":"ARTIFACT","description":"TaxonomicClassifier The taxonomic classifier for classifying the reads."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]"},{"names":["--p-pre-dispatch"],"argument":"TEXT","description":"\"all\" or expression, as in \"3*n_jobs\". The number of batches (of tasks) to be pre-dispatched."},{"names":["--p-read-orientation"],"argument":"TEXT Choices('same', 'reverse-complement', 'auto')","description":"Direction of reads with respect to reference sequences. same will cause reads to be classified unchanged; reverse-complement will cause reads to be reversed and complemented prior to classification. \"auto\" will autodetect orientation based on the confidence estimates for the first 100 reads."},{"names":["--o-classification"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"extract-reads","description":"Extract reads from reference sequences.","usage":"qiime feature-classifier extract-reads [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"[required]"},{"names":["--p-f-primer"],"argument":"TEXT","description":"forward primer sequence (5' -> 3'). [required]"},{"names":["--p-r-primer"],"argument":"TEXT","description":"reverse primer sequence (5' -> 3'). Do not use reverse-complemented primer sequence. [required]"},{"names":["--p-trim-right"],"argument":"INTEGER","description":"trim-right nucleotides are removed from the 3' end if trim-right is positive. Applied before trunc-len and trim-left. [default: 0]"},{"names":["--p-trunc-len"],"argument":"INTEGER","description":"read is cut to trunc-len if trunc-len is positive. Applied after trim-right but before trim-left."},{"names":["--p-trim-left"],"argument":"INTEGER","description":"trim-left nucleotides are removed from the 5' end if trim-left is positive. Applied after trim-right and trunc-len. [default: 0]"},{"names":["--p-identity"],"argument":"NUMBER","description":"minimum combined primer match identity threshold."},{"names":["--p-min-length"],"argument":"INTEGER","description":"Minimum amplicon length. Shorter amplicons are"},{"names":["--p-max-length"],"argument":"INTEGER","description":"Maximum amplicon length. Longer amplicons are"},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of seperate processes to run."},{"names":["--p-read-orientation"],"argument":"TEXT Choices('both', 'forward', 'reverse')","description":"Orientation of primers relative to the sequences: \"forward\" searches for primer hits in the forward direction, \"reverse\" searches reverse-complement, and \"both\" searches both directions."},{"names":["--o-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"find-consensus-annotation","description":"Find consensus among multiple annotations.","usage":"qiime feature-classifier find-consensus-annotation [OPTIONS]","options":[{"names":["--i-search-results"],"argument":"ARTIFACT FeatureData[BLAST6]","description":"Search results in BLAST6 output format [required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"reference taxonomy labels. [required]"},{"names":["--p-unassignable-label"],"argument":"TEXT","description":"Annotation given when no consensus is found."},{"names":["--o-consensus-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Consensus taxonomy and scores. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fit-classifier-naive-bayes","description":"Train the naive_bayes classifier","usage":"qiime feature-classifier fit-classifier-naive-bayes \n    [OPTIONS]","options":[{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"[required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--i-class-weight"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"[optional]"},{"names":["--p-classify--alpha"],"argument":"NUMBER","description":"[default: 0.001]"},{"names":["--p-classify--chunk-size"],"argument":"INTEGER","description":"[default: 20000]"},{"names":["--p-classify--fit-prior","--p-no-classify--fit-prior"],"argument":"","description":"[default: False]"},{"names":["--p-feat-ext--alternate-sign","--p-no-feat-ext--alternate-sign"],"argument":"","description":"[default: False]"},{"names":["--p-feat-ext--binary","--p-no-feat-ext--binary"],"argument":"","description":"[default: False]"},{"names":["--p-verbose","--p-no-verbose"],"argument":"","description":"[default: False]"},{"names":["--p-classify--class-prior"],"argument":"TEXT","description":"[default: 'null']"},{"names":["--p-feat-ext--analyzer"],"argument":"TEXT","description":"[default: 'char_wb']"},{"names":["--p-feat-ext--preprocessor"],"argument":"TEXT","description":"[default: 'null']"},{"names":["--p-feat-ext--stop-words"],"argument":"TEXT","description":"[default: 'null']"},{"names":["--p-feat-ext--strip-accents"],"argument":"TEXT","description":"[default: 'null']"},{"names":["--p-feat-ext--tokenizer"],"argument":"TEXT","description":"[default: 'null']"},{"names":["--p-feat-ext--decode-error"],"argument":"TEXT","description":"[default: 'strict']"},{"names":["--p-feat-ext--encoding"],"argument":"TEXT","description":"[default: 'utf-8']"},{"names":["--p-feat-ext--input"],"argument":"TEXT","description":"[default: 'content']"},{"names":["--p-feat-ext--lowercase","--p-no-feat-ext--lowercase"],"argument":"","description":"[default: True]"},{"names":["--p-feat-ext--n-features"],"argument":"INTEGER","description":"[default: 8192]"},{"names":["--p-feat-ext--ngram-range"],"argument":"TEXT","description":"[default: '[7, 7]']"},{"names":["--p-feat-ext--norm"],"argument":"TEXT","description":"[default: 'l2']"},{"names":["--p-feat-ext--token-pattern"],"argument":"TEXT","description":"[default: '(?u)\\\\b\\\\w\\\\w+\\\\b']"},{"names":["--o-classifier"],"argument":"ARTIFACT TaxonomicClassifier","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fit-classifier-sklearn","description":"Train an almost arbitrary scikit-learn classifier","usage":"qiime feature-classifier fit-classifier-sklearn [OPTIONS]","options":[{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"[required]"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--i-class-weight"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"[optional]"},{"names":["--p-classifier-specification"],"argument":"TEXT","description":"[required]"},{"names":["--o-classifier"],"argument":"ARTIFACT TaxonomicClassifier","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"makeblastdb","description":"Make BLAST database.","usage":"qiime feature-classifier makeblastdb [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Input reference sequences. [required]"},{"names":["--o-database"],"argument":"ARTIFACT","description":"Output BLAST database."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"vsearch-global","description":"VSEARCH global alignment search","usage":"qiime feature-classifier vsearch-global [OPTIONS]","options":[{"names":["--i-query"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query Sequences. [required]"},{"names":["--i-reference-reads"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences. [required]"},{"names":["--p-perc-identity"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if percent identity to query is lower."},{"names":["--p-query-cov"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8]"},{"names":["--p-strand"],"argument":"TEXT Choices('both', 'plus')","description":"Align against reference sequences in forward (\"plus\") or both directions (\"both\")."},{"names":["--p-search-exact","--p-no-search-exact"],"argument":"","description":"Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity, query-cov, maxaccepts, and maxrejects settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False]"},{"names":["--p-top-hits-only","--p-no-top-hits-only"],"argument":"","description":"Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False]"},{"names":["--p-output-no-hits","--p-no-output-no-hits"],"argument":"","description":"Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs."},{"names":["--p-weak-id"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0]"},{"names":["--p-threads"],"argument":"NTHREADS","description":"Number of threads to use for job parallelization. Pass 0 to use one per available CPU. [default: 1]"},{"names":["--o-search-results"],"argument":"ARTIFACT","description":"FeatureData[BLAST6] Top hits for each query. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"feature-table","description":"Plugin for working with sample by feature tables.","usage":"qiime feature-table [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"core-features","description":"Identify core features in table","usage":"qiime feature-table core-features [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to use in core features calculations. [required]"},{"names":["--p-min-fraction"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 0.5]"},{"names":["--p-max-fraction"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 1.0]"},{"names":["--p-steps"],"argument":"INTEGER","description":"The number of steps to take between `min-fraction` and"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-features","description":"Filter features from table","usage":"qiime feature-table filter-features [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table from which features should be filtered. [required]"},{"names":["--p-min-frequency"],"argument":"INTEGER","description":"The minimum total frequency that a feature must have to be retained. [default: 0]"},{"names":["--p-max-frequency"],"argument":"INTEGER","description":"The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]"},{"names":["--p-min-samples"],"argument":"INTEGER","description":"The minimum number of samples that a feature must be observed in to be retained. [default: 0]"},{"names":["--p-max-samples"],"argument":"INTEGER","description":"The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied). [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Feature metadata used with `where` parameter when selecting features to retain, or with `exclude-ids` when selecting features to discard."},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the feature table will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"If true, the features selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. [default: False]"},{"names":["--p-filter-empty-samples","--p-no-filter-empty-samples"],"argument":"","description":"If true, drop any samples where none of the retained features are present. [default: True]"},{"names":["--p-allow-empty-table","--p-no-allow-empty-table"],"argument":"","description":"If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]"},{"names":["--o-filtered-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting feature table filtered by feature. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-features-conditionally","description":"Filter features from a table based on abundance and prevalence","usage":"qiime feature-table filter-features-conditionally [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"The feature table from which features should be filtered. [required]"},{"names":["--p-abundance"],"argument":"PROPORTION","description":"The minimum relative abundance for a feature to be retained. [required]"},{"names":["--p-prevalence"],"argument":"PROPORTION","description":"The minimum portion of samples that a feature must have a relative abundance of at least `abundance` to be retained. [required]"},{"names":["--p-allow-empty-table","--p-no-allow-empty-table"],"argument":"","description":"If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]"},{"names":["--o-filtered-table"],"argument":"ARTIFACT","description":"The resulting feature table filtered by feature. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-samples","description":"Filter samples from table","usage":"qiime feature-table filter-samples [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"The feature table from which samples should be filtered. [required]"},{"names":["--p-min-frequency"],"argument":"INTEGER","description":"The minimum total frequency that a sample must have to be retained. [default: 0]"},{"names":["--p-max-frequency"],"argument":"INTEGER","description":"The maximum total frequency that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]"},{"names":["--p-min-features"],"argument":"INTEGER","description":"The minimum number of features that a sample must have to be retained. [default: 0]"},{"names":["--p-max-features"],"argument":"INTEGER","description":"The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied). [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude-ids` when selecting samples to discard."},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"If true, the samples selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. [default: False]"},{"names":["--p-filter-empty-features","--p-no-filter-empty-features"],"argument":"","description":"If true, features which are not present in any retained samples are dropped. [default: True]"},{"names":["--p-allow-empty-table","--p-no-allow-empty-table"],"argument":"","description":"If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]"},{"names":["--o-filtered-table"],"argument":"ARTIFACT","description":"The resulting feature table filtered by sample. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-seqs","description":"Filter features from sequences","usage":"qiime feature-table filter-seqs [OPTIONS]","options":[{"names":["--i-data"],"argument":"ARTIFACT FeatureData[Sequence¹ | AlignedSequence²]","description":"The sequences from which features should be filtered. [required]"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Table containing feature ids used for id-based filtering. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Feature metadata used for id-based filtering, with `where` parameter when selecting features to retain, or with `exclude-ids` when selecting features to discard."},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences will be retained. [optional]"},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained. [default: False]"},{"names":["--o-filtered-data"],"argument":"ARTIFACT FeatureData[Sequence¹ | AlignedSequence²]","description":"The resulting filtered sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"group","description":"Group samples or features by a metadata column","usage":"qiime feature-table group [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The table to group samples or features on. [required]"},{"names":["--p-axis"],"argument":"TEXT Choices('feature', 'sample')","description":"Along which axis to group. Each ID in the given axis must exist in `metadata`. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"A column defining the groups. Each unique value will become a new ID for the table on the given `axis`."},{"names":["--p-mode"],"argument":"TEXT Choices('mean-ceiling', 'median-ceiling', 'sum')","description":"How to combine samples or features within a group. `sum` will sum the frequencies across all samples or features within a group; `mean-ceiling` will take the ceiling of the mean of these frequencies; `median-ceiling` will take the ceiling of the median of these frequencies. [required]"},{"names":["--o-grouped-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"A table that has been grouped along the given `axis`. IDs on that axis are replaced by values in the `metadata` column. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"heatmap","description":"Generate a heatmap representation of a feature table","usage":"qiime feature-table heatmap [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to visualize. [required]"},{"names":["--m-sample-metadata-file"],"argument":"","description":"METADATA"},{"names":["--m-sample-metadata-column"],"argument":"COLUMN  MetadataColumn[Categorical]","description":"Annotate the sample IDs with these sample metadata values. When metadata is present and `cluster`='feature', samples will be sorted by the metadata values. [optional]"},{"names":["--m-feature-metadata-file"],"argument":"","description":"METADATA"},{"names":["--m-feature-metadata-column"],"argument":"COLUMN  MetadataColumn[Categorical]","description":"Annotate the feature IDs with these feature metadata values. When metadata is present and `cluster`='sample', features will be sorted by the metadata values. [optional]"},{"names":["--p-normalize","--p-no-normalize"],"argument":"","description":"Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table."},{"names":["--p-title"],"argument":"TEXT","description":"Optional custom plot title. [optional]"},{"names":["--p-cluster"],"argument":"TEXT Choices('both', 'features', 'none', 'samples')","description":"Specify which axes to cluster. [default: 'both']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"merge","description":"Combine multiple tables","usage":"qiime feature-table merge [OPTIONS]","options":[{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"merge-seqs","description":"Combine collections of feature sequences","usage":"qiime feature-table merge-seqs [OPTIONS]","options":[{"names":["--i-data"],"argument":"ARTIFACTS... List[FeatureData[Sequence]]","description":"The collection of feature sequences to be merged."},{"names":["--o-merged-data"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting collection of feature sequences containing all feature sequences provided. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"merge-taxa","description":"Combine collections of feature taxonomies","usage":"qiime feature-table merge-taxa [OPTIONS]","options":[{"names":["--i-data"],"argument":"ARTIFACTS... List[FeatureData[Taxonomy]]","description":"The collection of feature taxonomies to be merged."},{"names":["--o-merged-data"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"The resulting collection of feature taxonomies containing all feature taxonomies provided."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"presence-absence","description":"Convert to presence/absence","usage":"qiime feature-table presence-absence [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | RelativeFrequency]","description":"The feature table to be converted into presence/absence abundances. [required]"},{"names":["--o-presence-absence-table"],"argument":"ARTIFACT FeatureTable[PresenceAbsence]","description":"The resulting presence/absence feature table."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"rarefy","description":"Rarefy table","usage":"qiime feature-table rarefy [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to be rarefied. [required]"},{"names":["--p-sampling-depth"],"argument":"INTEGER","description":"The total frequency that each sample should be rarefied to. [required]"},{"names":["--p-with-replacement","--p-no-with-replacement"],"argument":"","description":"Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]"},{"names":["--o-rarefied-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting rarefied feature table. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"relative-frequency","description":"Convert to relative frequencies","usage":"qiime feature-table relative-frequency [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to be converted into relative frequencies. [required]"},{"names":["--o-relative-frequency-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"The resulting relative frequency feature table."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"rename-ids","description":"Renames sample or feature ids in a table","usage":"qiime feature-table rename-ids [OPTIONS]","options":[{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"A metadata column defining the new ids. Each original id must map to a new unique id. If strict mode is used, then every id in the original table must have a new id."},{"names":["--p-axis"],"argument":"TEXT Choices('feature', 'sample')","description":"Along which axis to rename the ids. [default: 'sample']"},{"names":["--p-strict","--p-no-strict"],"argument":"","description":"Whether the naming needs to be strict (each id in the table must have a new id). Otherwise, only the ids described in `metadata` will be renamed and the others will keep their original id names. [default: False]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"split","description":"Split one feature table into many","usage":"qiime feature-table split [OPTIONS]","options":[{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"A column defining the groups. Each unique value will define a split feature table. [required]"},{"names":["--p-filter-empty-features","--p-no-filter-empty-features"],"argument":"","description":"If true, features which are not present in a split feature table are dropped. [default: True]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"subsample-ids","description":"Subsample table","usage":"qiime feature-table subsample-ids [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to be sampled. [required]"},{"names":["--p-subsampling-depth"],"argument":"","description":"INTEGER"},{"names":["--p-axis"],"argument":"TEXT Choices('sample', 'feature')","description":"The axis to sample over. If \"sample\" then samples will be randomly selected to be retained. If \"feature\" then a random set of features will be selected to be retained. [required]"},{"names":["--o-sampled-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting subsampled feature table. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"summarize","description":"Summarize table","usage":"qiime feature-table summarize [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | PresenceAbsence]","description":"The feature table to be summarized. [required]"},{"names":["--m-sample-metadata-file"],"argument":"METADATA...","description":"The sample metadata."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"summarize-plus","description":"Summarize table plus","usage":"qiime feature-table summarize-plus [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | PresenceAbsence]","description":"The feature table to be summarized. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata."},{"names":["--o-feature-frequencies"],"argument":"ARTIFACT","description":"Per-sample and total frequencies per feature. [required]"},{"names":["--o-sample-frequencies"],"argument":"ARTIFACT","description":"Observed feature count and total frequencies per sample. [required]"},{"names":["--o-summary"],"argument":"VISUALIZATION","description":"Visual summary of feature table [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. 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[required]"},{"names":["--o-feature-frequencies"],"argument":"ARTIFACT","description":"ImmutableMetadata Per-sample and total frequencies per feature."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tabulate-sample-frequencies","description":"Tabulate sample frequencies","usage":"qiime feature-table tabulate-sample-frequencies [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"The input feature table. [required]"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTableFrequency | PresenceAbsence |   RelativeFrequency","description":"The input feature table. [required]"},{"names":["--o-sample-frequencies"],"argument":"ARTIFACT","description":"ImmutableMetadata Observed feature count and total frequencies per"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"tabulate-seqs","description":"View sequence associated with each feature","usage":"qiime feature-table tabulate-seqs [OPTIONS]","options":[{"names":["--i-data"],"argument":"ARTIFACT FeatureData[Sequence | AlignedSequence]","description":"The feature sequences to be tabulated. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACTS... Collection[FeatureData[Taxonomy]]","description":"The taxonomic classifications of the tabulated features. [optional]"},{"names":["--p-merge-method"],"argument":"TEXT Choices('strict', 'union', 'intersect')","description":"Method that joins data sets [default: 'strict']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Any additional metadata for the tabulated features."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"transpose","description":"Transpose a feature table.","usage":"qiime feature-table transpose [OPTIONS]","options":[{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"fondue","description":"Plugin for fetching sequences and metadata.","usage":"qiime fondue [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"combine-seqs","description":"Combine sequences from multiple artifacts.","usage":"qiime fondue combine-seqs [OPTIONS]","options":[{"names":["--i-seqs"],"argument":"ARTIFACT...","description":"Sequence artifacts to be combined together. [required]"},{"names":["--p-on-duplicates"],"argument":"TEXT Choices('error', 'warn')","description":"Preferred behaviour when duplicated sequence IDs are encountered: \"warn\" displays a warning and continues to combining deduplicated samples while \"error\" raises an error and aborts further execution. [default: 'error']"},{"names":["--o-combined-seqs"],"argument":"ARTIFACT","description":"Sequences combined from all input artifacts. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-all","description":"Fetch sequence-related metadata and sequences of all run, study, BioProject, experiment or sample IDs.","usage":"qiime fondue get-all [OPTIONS]","options":[{"names":["--i-accession-ids"],"argument":"ARTIFACT","description":"Artifact containing run, study, BioProject, experiment or sample IDs for which the metadata and/or sequences should be fetched. Associated DOI names can be providedin an optional column and are preserved in get-alland get-metadata actions. [required]"},{"names":["--i-linked-doi"],"argument":"ARTIFACT","description":"Optional table containing linked DOI names that is only used if accession-ids does not contain any DOI names."},{"names":["--p-email"],"argument":"TEXT","description":"Your e-mail address (required by NCBI). [required]"},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of concurrent download jobs."},{"names":["--p-retries"],"argument":"INTEGER","description":"Number of retries to fetch sequences."},{"names":["--p-log-level"],"argument":"TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')","description":"Logging level. [default: 'INFO']"},{"names":["--o-metadata"],"argument":"ARTIFACT","description":"Table containing metadata for all the requested"},{"names":["--o-single-reads"],"argument":"ARTIFACT","description":"Artifact containing single-read fastq.gz files for all the requested IDs. [required]"},{"names":["--o-paired-reads"],"argument":"ARTIFACT","description":"Artifact containing paired-end fastq.gz files for all the requested IDs. [required]"},{"names":["--o-failed-runs"],"argument":"ARTIFACT","description":"List of all run IDs for which fetching sequences and/or metadata  failed, with their corresponding error messages. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-ids-from-query","description":"Find SRA run accession IDs based on a search query.","usage":"qiime fondue get-ids-from-query [OPTIONS]","options":[{"names":["--p-query"],"argument":"TEXT","description":"Search query to retrieve SRA run IDs from the BioSample database. [required]"},{"names":["--p-email"],"argument":"TEXT","description":"Your e-mail address (required by NCBI). [required]"},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of concurrent download jobs."},{"names":["--p-log-level"],"argument":"TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')","description":"Logging level. [default: 'INFO']"},{"names":["--o-ids"],"argument":"ARTIFACT","description":"Table containing metadata for all the requested IDs.  [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-metadata","description":"Fetch sequence-related metadata based on run, study, BioProject, experiment or sample ID.","usage":"qiime fondue get-metadata [OPTIONS]","options":[{"names":["--i-accession-ids"],"argument":"ARTIFACT","description":"Artifact containing run, study, BioProject, experiment or sample IDs for which the metadata and/or sequences should be fetched. 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[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-sequences","description":"Fetch sequences based on run ID.","usage":"qiime fondue get-sequences [OPTIONS]","options":[{"names":["--i-accession-ids"],"argument":"ARTIFACT","description":"Artifact containing run, study, BioProject, experiment or sample IDs for which the metadata and/or sequences should be fetched. Associated DOI names can be providedin an optional column and are preserved in get-alland get-metadata actions."},{"names":["--p-email"],"argument":"TEXT","description":"Your e-mail address (required by NCBI). [required]"},{"names":["--p-retries"],"argument":"INTEGER","description":"Number of retries to fetch sequences."},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of concurrent download jobs."},{"names":["--p-log-level"],"argument":"TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')","description":"Logging level. [default: 'INFO']"},{"names":["--p-restricted-access","--p-no-restricted-access"],"argument":"","description":"If sequence fetch requires dbGaP repository key."},{"names":["--o-single-reads"],"argument":"ARTIFACT SampleData[SequencesWithQuality]","description":"Artifact containing single-read fastq.gz files for all the requested IDs. [required]"},{"names":["--o-paired-reads"],"argument":"ARTIFACT SampleData[PairedEndSequencesWithQuality]","description":"Artifact containing paired-end fastq.gz files for all the requested IDs. [required]"},{"names":["--o-failed-runs"],"argument":"ARTIFACT","description":"List of all run IDs for which fetching sequences failed, with their corresponding error messages. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"merge-metadata","description":"Merge several metadata files into a single metadata object.","usage":"qiime fondue merge-metadata [OPTIONS]","options":[{"names":["--i-metadata"],"argument":"ARTIFACTS...","description":"Metadata files to be merged together. [required]"},{"names":["--o-merged-metadata"],"argument":"ARTIFACT","description":"Merged metadata containing all rows and columns (without duplicates). [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"scrape-collection","description":"Scrape Zotero collection for run, study, BioProject, experiment and sample IDs, and associated DOI names.","usage":"qiime fondue scrape-collection [OPTIONS]","options":[{"names":["--p-collection-name"],"argument":"TEXT","description":"Name of the collection to be scraped. [required]"},{"names":["--p-on-no-dois"],"argument":"TEXT Choices('ignore', 'error')","description":"Behavior if no DOIs were found. [default: 'ignore']"},{"names":["--p-log-level"],"argument":"TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')","description":"Logging level. [default: 'INFO']"},{"names":["--o-run-ids"],"argument":"ARTIFACT","description":"Artifact containing all run IDs scraped from a Zotero collection and associated DOI names. [required]"},{"names":["--o-study-ids"],"argument":"ARTIFACT","description":"Artifact containing all study IDs scraped from a Zotero collection and associated DOI names. [required]"},{"names":["--o-bioproject-ids"],"argument":"ARTIFACT","description":"Artifact containing all BioProject IDs scraped from a Zotero collection and associated DOI names. [required]"},{"names":["--o-experiment-ids"],"argument":"ARTIFACT","description":"Artifact containing all experiment IDs scraped from a Zotero collection and associated DOI names. [required]"},{"names":["--o-sample-ids"],"argument":"ARTIFACT","description":"Artifact containing all experiment IDs scraped from a Zotero collection and associated DOI names. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"fragment-insertion","description":"Plugin for extending phylogenies.","usage":"qiime fragment-insertion [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"classify-otus-experimental","description":"Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.","usage":"qiime fragment-insertion classify-otus-experimental [OPTIONS]","options":[{"names":["--i-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences used for a 'sepp' run to produce the 'tree'. [required]"},{"names":["--i-tree"],"argument":"ARTIFACT","description":"The tree resulting from inserting fragments into a"},{"names":["--i-reference-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string. [required]"},{"names":["--o-classification"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic lineages for inserted fragments. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-features","description":"Filter fragments in tree from table.","usage":"qiime fragment-insertion filter-features [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"A feature-table which needs to filtered down to those fragments that are contained in the tree, e.g. result of a Deblur or DADA2 run. [required]"},{"names":["--i-tree"],"argument":"ARTIFACT","description":"The tree resulting from inserting fragments into a"},{"names":["--o-filtered-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The input table minus those fragments that were not part of the tree. This feature-table can be used for downstream analyses like phylogenetic alpha- or betadiversity computation. [required]"},{"names":["--o-removed-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Those fragments that got removed from the input table, because they were not part of the tree. This table is mainly used for quality control, e.g. to inspect the ratio of removed reads per sample from the input table. You can ignore this table for downstream analyses."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"sepp","description":"Insert fragment sequences using SEPP into reference phylogenies.","usage":"qiime fragment-insertion sepp [OPTIONS]","options":[{"names":["--i-representative-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to insert into the reference tree."},{"names":["--i-reference-database"],"argument":"ARTIFACT SeppReferenceDatabase","description":"The reference database to insert the representative sequences into. [required]"},{"names":["--p-alignment-subset-size"],"argument":"INTEGER","description":"Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. [default: 1000]"},{"names":["--p-placement-subset-size"],"argument":"INTEGER","description":"The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. Further reading: https://github.com/smirarab/sepp/blob/master/tutorial/ sepp-tutorial.md#sample-datasets-default-parameters."},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of threads to use. Pass 0 to use one per available core. [default: 1]"},{"names":["--p-debug","--p-no-debug"],"argument":"","description":"Collect additional run information to STDOUT for debugging. Temporary directories will not be removed if run fails. [default: False]"},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The tree with inserted feature data."},{"names":["--o-placements"],"argument":"ARTIFACT","description":"Placements Information about the feature placements within the"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"longitudinal","description":"Plugin for paired sample and time series analyses.","usage":"qiime longitudinal [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"anova","description":"ANOVA test","usage":"qiime longitudinal anova [OPTIONS]","options":[{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata containing formula terms. [required]"},{"names":["--p-formula"],"argument":"TEXT","description":"R-style formula specifying the model. All terms must be present in the sample metadata or metadata-transformable artifacts and can be continuous or categorical metadata columns. Formulae will be in the format \"a ~ b + c\", where \"a\" is the metric (dependent variable) and \"b\" and \"c\" are independent covariates. Use \"+\" to add a variable; \"+ a:b\" to add an interaction between variables a and b; \"*\" to include a variable and all interactions; and \"-\" to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [required]"},{"names":["--p-sstype"],"argument":"TEXT Choices('I', 'II', 'III')","description":"Type of sum of squares calculation to perform (I, II, or III). [default: 'II']"},{"names":["--p-repeated-measures","--p-no-repeated-measures"],"argument":"","description":"Perform ANOVA as a repeated measures ANOVA. Implemented via statsmodels, which has the following limitations: Currently, only fully balanced within-subject designs are supported. Calculation of between-subject effects and corrections for violation of sphericity are not yet implemented. [default: False]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"The column containing individual ID with repeated measures to account for.This should not be included in the formula. [optional]"},{"names":["--p-rm-aggregate","--p-no-rm-aggregate"],"argument":"","description":"If the data set contains more than a single observation per individual id and cell of the specified model, this function will be used to aggregate the data by the mean before running the ANOVA. Only applicable for repeated measures ANOVA. [default: False]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"feature-volatility","description":"Feature volatility analysis","usage":"qiime longitudinal feature-volatility [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata containing collection time (state) values for each sample. Must contain exclusively numeric values. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [optional]"},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation. More trees will improve predictive accuracy up to a threshold level, but will also increase time and memory requirements."},{"names":["--p-estimator"],"argument":"{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor, ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}","description":"Estimator method to use for sample prediction."},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--p-importance-threshold"],"argument":"VALUE","description":"Filter feature table to exclude any features with an importance score less than this threshold."},{"names":["--p-feature-count"],"argument":"VALUE","description":"Filter feature table to include top N most important features."},{"names":["--o-filtered-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table containing only important features. [required]"},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy. [required]"},{"names":["--o-volatility-plot"],"argument":"VISUALIZATION","description":"Interactive volatility plot visualization. [required]"},{"names":["--o-accuracy-results"],"argument":"VISUALIZATION","description":"Accuracy results visualization. [required]"},{"names":["--o-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Regressor]","description":"Trained sample regressor. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"first-differences","description":"Compute first differences or difference from","usage":"qiime longitudinal first-differences [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table to optionally use for computing first differences. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (time) variable information. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"Numerical metadata or artifact column to test."},{"names":["--p-replicate-handling"],"argument":"TEXT Choices('error', 'random', 'drop')","description":"Choose how replicate samples are handled. If replicates are detected, \"error\" causes method to fail; \"drop\" will discard all replicated samples; \"random\" chooses one representative at random from among replicates. [default: 'error']"},{"names":["--p-baseline"],"argument":"NUMBER","description":"A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static differences instead of first differences (which are calculated if no value is given for baseline). If a \"baseline\" value is provided, sample differences at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]"},{"names":["--o-first-differences"],"argument":"ARTIFACT SampleData[FirstDifferences]","description":"Series of first differences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"first-distances","description":"Compute first distances or distance from baseline","usage":"qiime longitudinal first-distances [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (time) variable information. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [required]"},{"names":["--p-baseline"],"argument":"NUMBER","description":"A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a \"baseline\" value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column."},{"names":["--p-replicate-handling"],"argument":"TEXT Choices('error', 'random', 'drop')","description":"Choose how replicate samples are handled. If replicates are detected, \"error\" causes method to fail; \"drop\" will discard all replicated samples; \"random\" chooses one representative at random from among replicates. [default: 'error']"},{"names":["--o-first-distances"],"argument":"ARTIFACT SampleData[FirstDifferences]","description":"Series of first distances. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"linear-mixed-effects","description":"Linear mixed effects modeling","usage":"qiime longitudinal linear-mixed-effects [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table containing metric. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (time) variable information. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"Dependent variable column name. Must be a column name located in the metadata or feature table files."},{"names":["--p-group-columns"],"argument":"TEXT","description":"Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine mean structure of \"metric\". [optional]"},{"names":["--p-random-effects"],"argument":"TEXT","description":"Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine the variance and covariance structure (random effects) of \"metric\". To add a random slope, the same value passed to \"state-column\" should be passed here. A random intercept for each individual is set by default and does not need to be passed here. [optional]"},{"names":["--p-palette"],"argument":"TEXT","description":"Color palette to use for generating boxplots."},{"names":["--p-lowess","--p-no-lowess"],"argument":"","description":"Estimate locally weighted scatterplot smoothing. Note that this will eliminate confidence interval plotting. [default: False]"},{"names":["--p-ci"],"argument":"NUMBER","description":"Size of the confidence interval for the regression"},{"names":["--p-formula"],"argument":"TEXT","description":"R-style formula to use for model specification. A formula must be used if the \"metric\" parameter is None. Note that the metric and group columns specified in the formula will override metric and group columns that are passed separately as parameters to this method. Formulae will be in the format \"a ~ b + c\", where \"a\" is the metric (dependent variable) and \"b\" and \"c\" are independent covariates. Use \"+\" to add a variable; \"+ a:b\" to add an interaction between variables a and b; \"*\" to include a variable and all interactions; and \"-\" to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [optional]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"maturity-index","description":"Microbial maturity index prediction.","usage":"qiime longitudinal maturity-index [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"metadata file(s) [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Numeric metadata column containing sampling time (state) data to use as prediction target. [required]"},{"names":["--p-group-by"],"argument":"TEXT","description":"Categorical metadata column to use for plotting and significance testing between main treatment groups. [required]"},{"names":["--p-control"],"argument":"TEXT","description":"Value of group-by to use as control group. The regression model will be trained using only control group data, and the maturity scores of other groups consequently will be assessed relative to this group. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Optional metadata column containing IDs for individual subjects. Adds individual subject (spaghetti) vectors to volatility charts if a column name is provided. [optional]"},{"names":["--p-estimator"],"argument":"{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor[DecisionTree], AdaBoostRegressor[ExtraTrees], ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}","description":"Regression model to use for prediction."},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-test-size"],"argument":"PROPORTION","description":"Fraction of input samples to exclude from training set and use for classifier testing."},{"names":["--p-step"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"If optimize-feature-selection is True, step is the percentage of features to remove at each iteration."},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-optimize-feature-selection","--p-no-optimize-feature-selection"],"argument":"","description":"Automatically optimize input feature selection using recursive feature elimination."},{"names":["--p-stratify","--p-no-stratify"],"argument":"","description":"Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: False]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--p-feature-count"],"argument":"INTEGER","description":"Filter feature table to include top N most important features."},{"names":["--o-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Regressor]","description":"Trained sample estimator. [required]"},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy. [required]"},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[RegressorPredictions]","description":"Predicted target values for each input sample. [required]"},{"names":["--o-model-summary"],"argument":"VISUALIZATION","description":"Summarized parameter and (if enabled) feature selection information for the trained estimator. [required]"},{"names":["--o-accuracy-results"],"argument":"VISUALIZATION","description":"Accuracy results visualization. [required]"},{"names":["--o-maz-scores"],"argument":"ARTIFACT SampleData[RegressorPredictions]","description":"Microbiota-for-age z-score predictions. [required]"},{"names":["--o-clustermap"],"argument":"VISUALIZATION","description":"Heatmap of important feature abundance at each time point in each group. [required]"},{"names":["--o-volatility-plots"],"argument":"VISUALIZATION","description":"Interactive volatility plots of MAZ and maturity scores, target (column) predictions, and the sample metadata. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"nmit","description":"Nonparametric microbial interdependence test","usage":"qiime longitudinal nmit [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table to use for microbial interdependence test. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [required]"},{"names":["--p-corr-method"],"argument":"TEXT Choices('kendall', 'pearson', 'spearman')","description":"The temporal correlation test to be applied."},{"names":["--p-dist-method"],"argument":"TEXT Choices('fro', 'nuc')","description":"Temporal distance method, see numpy.linalg.norm for details. [default: 'fro']"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix The resulting distance matrix. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"pairwise-differences","description":"Paired difference testing and boxplots","usage":"qiime longitudinal pairwise-differences [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table to optionally use for paired comparisons. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-metric"],"argument":"TEXT","description":"Numerical metadata or artifact column to test. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (e.g., Time) across which samples are paired. [required]"},{"names":["--p-state-1"],"argument":"TEXT","description":"Baseline state column value. [required]"},{"names":["--p-state-2"],"argument":"TEXT","description":"State column value to pair with baseline. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling=\"random\" to instead randomly select one member. [required]"},{"names":["--p-group-column"],"argument":"TEXT","description":"Metadata column on which to separate groups for comparison [optional]"},{"names":["--p-parametric","--p-no-parametric"],"argument":"","description":"Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests."},{"names":["--p-replicate-handling"],"argument":"TEXT Choices('error', 'random', 'drop')","description":"Choose how replicate samples are handled. If replicates are detected, \"error\" causes method to fail; \"drop\" will discard all replicated samples; \"random\" chooses one representative at random from among replicates. [default: 'error']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"pairwise-distances","description":"Paired pairwise distance testing and boxplots","usage":"qiime longitudinal pairwise-distances [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"Matrix of distances between pairs of samples. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-group-column"],"argument":"TEXT","description":"Metadata column on which to separate groups for comparison [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (e.g., Time) across which samples are paired. [required]"},{"names":["--p-state-1"],"argument":"TEXT","description":"Baseline state column value. [required]"},{"names":["--p-state-2"],"argument":"TEXT","description":"State column value to pair with baseline. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling=\"random\" to instead randomly select one member. [required]"},{"names":["--p-parametric","--p-no-parametric"],"argument":"","description":"Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests."},{"names":["--p-replicate-handling"],"argument":"TEXT Choices('error', 'random', 'drop')","description":"Choose how replicate samples are handled. If replicates are detected, \"error\" causes method to fail; \"drop\" will discard all replicated samples; \"random\" chooses one representative at random from among replicates. [default: 'error']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"plot-feature-volatility","description":"Plot longitudinal feature volatility and importances","usage":"qiime longitudinal plot-feature-volatility [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table containing features found in importances. [required]"},{"names":["--i-importances"],"argument":"ARTIFACT FeatureData[Importance]","description":"Feature importance scores. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (time) variable information. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. [optional]"},{"names":["--p-default-group-column"],"argument":"TEXT","description":"The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization)."},{"names":["--p-yscale"],"argument":"TEXT Choices('linear', 'pow', 'sqrt', 'log')","description":"y-axis scaling strategy to apply. [default: 'linear']"},{"names":["--p-importance-threshold"],"argument":"VALUE","description":"Filter feature table to exclude any features with an importance score less than this threshold."},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"volatility","description":"Generate interactive volatility plot","usage":"qiime longitudinal volatility [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Feature table containing metrics. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata file containing individual-id-column. [required]"},{"names":["--p-state-column"],"argument":"TEXT","description":"Metadata column containing state (time) variable information. [required]"},{"names":["--p-individual-id-column"],"argument":"TEXT","description":"Metadata column containing IDs for individual subjects. 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Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"eggnog-diamond-search","description":"Run eggNOG search using diamond aligner","usage":"qiime moshpit eggnog-diamond-search [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT","description":"Sequence data of the contigs we want to search for hits using the Diamond Database [required]"},{"names":["--i-diamond-db"],"argument":"ARTIFACT","description":"The filepath to an artifact containing the Diamond database [required]"},{"names":["--p-num-cpus"],"argument":"INTEGER","description":"Number of CPUs to utilize. '0' will use all available. [default: 1]"},{"names":["--p-db-in-memory","--p-no-db-in-memory"],"argument":"","description":"Read database into memory. The database can be very large, so this option should only be used on clusters or other machines with enough memory."},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the contigs into."},{"names":["--o-table"],"argument":"ARTIFACT","description":"[required]"},{"names":["--o-eggnog-hits"],"argument":"ARTIFACT","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"estimate-bracken","description":"Perform read abundance re-estimation using Bracken.","usage":"qiime moshpit estimate-bracken [OPTIONS]","options":[{"names":["--i-kraken-reports"],"argument":"ARTIFACT SampleData","description":"Reports produced by Kraken2. [required]"},{"names":["--i-bracken-db"],"argument":"ARTIFACT","description":"BrackenDB Bracken database. [required]"},{"names":["--p-threshold"],"argument":"INTEGER","description":"Bracken: number of reads required PRIOR to abundance estimation to perform re-estimation."},{"names":["--p-read-len"],"argument":"INTEGER","description":"Bracken: read length to get all classifications for."},{"names":["--p-level"],"argument":"TEXT Choices('D', 'P', 'C', 'O', 'F', 'G', 'S')","description":"Bracken: taxonomic level to estimate abundance at."},{"names":["--o-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--o-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"[required]"},{"names":["--o-reports"],"argument":"ARTIFACT SampleData[Kraken2Report % Properties('bracken')]","description":"Reports modified by Bracken. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-busco","description":"Evaluate quality of the generated MAGs using BUSCO.","usage":"qiime moshpit evaluate-busco [OPTIONS]","options":[{"names":["--i-bins"],"argument":"ARTIFACT","description":"MAGs to be analyzed. [required]"},{"names":["--p-mode"],"argument":"TEXT","description":"Specify which BUSCO analysis mode to run."},{"names":["--p-lineage-dataset"],"argument":"TEXT","description":"Specify the name of the BUSCO lineage to be used. To see all possible options run `busco --list-datasets`. [optional]"},{"names":["--p-augustus","--p-no-augustus"],"argument":"","description":"Use augustus gene predictor for eukaryote runs."},{"names":["--p-augustus-parameters"],"argument":"TEXT","description":"Pass additional arguments to Augustus. All arguments should be contained within a single string with no white space, with each argument separated by a comma. Example: '--PARAM1=VALUE1,--PARAM2=VALUE2'."},{"names":["--p-augustus-species"],"argument":"TEXT","description":"Specify a species for Augustus training. [optional]"},{"names":["--p-auto-lineage","--p-no-auto-lineage"],"argument":"","description":"Run auto-lineage to find optimum lineage path."},{"names":["--p-auto-lineage-euk","--p-no-auto-lineage-euk"],"argument":"","description":"Run auto-placement just on eukaryote tree to find optimum lineage path. [default: False]"},{"names":["--p-auto-lineage-prok","--p-no-auto-lineage-prok"],"argument":"","description":"Run auto-lineage just on non-eukaryote trees to find optimum lineage path. [default: False]"},{"names":["--p-cpu"],"argument":"INTEGER","description":"Specify the number (N=integer) of threads/cores to use."},{"names":["--p-config"],"argument":"TEXT","description":"Provide a config file. [optional]"},{"names":["--p-contig-break"],"argument":"INTEGER","description":"Number of contiguous Ns to signify a break between contigs."},{"names":["--p-evalue"],"argument":"NUMBER","description":"E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03, Default: 1e-03. [default: 0.001]"},{"names":["--p-force","--p-no-force"],"argument":"","description":"Force rewriting of existing files. Must be used when output files with the provided name already exist. [default: False]"},{"names":["--p-limit"],"argument":"INTEGER","description":"How many candidate regions (contig or transcript) to consider per BUSCO."},{"names":["--p-long","--p-no-long"],"argument":"","description":"Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms."},{"names":["--p-metaeuk-parameters"],"argument":"TEXT","description":"Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single string with no white space, with each argument separated by a comma. Example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. [optional]"},{"names":["--p-metaeuk-rerun-parameters"],"argument":"TEXT","description":"Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma. Example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. [optional]"},{"names":["--p-miniprot","--p-no-miniprot"],"argument":"","description":"Use miniprot gene predictor for eukaryote runs."},{"names":["--p-scaffold-composition","--p-no-scaffold-composition"],"argument":"","description":"Writes ACGTN content per scaffold to a file `scaffold_composition.txt`. [default: False]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the contigs into."},{"names":["--o-results-table"],"argument":"ARTIFACT","description":"BUSCO result table. [required]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"Visualization of the BUSCO results. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fetch-diamond-db","description":"Fetch the complete Diamond database necessary to run the eggnog-diamond-search action.","usage":"qiime moshpit fetch-diamond-db [OPTIONS]","options":[{"names":["--o-diamond-db"],"argument":"ARTIFACT","description":"Complete Diamond reference database. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fetch-eggnog-db","description":"Fetch the databases necessary to run the eggnog-annotate action.","usage":"qiime moshpit fetch-eggnog-db [OPTIONS]","options":[{"names":["--o-eggnog-db"],"argument":"ARTIFACT","description":"Artifact containing the eggNOG annotation database. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fetch-eggnog-proteins","description":"Fetch the databases necessary to run the build-eggnog-diamond-db action.","usage":"qiime moshpit fetch-eggnog-proteins [OPTIONS]","options":[{"names":["--o-eggnog-proteins"],"argument":"ARTIFACT","description":"eggNOG database of protein sequences and their corresponding taxonomy information. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fetch-kaiju-db","description":"Fetch Kaiju database.","usage":"qiime moshpit fetch-kaiju-db [OPTIONS]","options":[{"names":["--p-database-type"],"argument":"{nr, nr_euk, refseq, fungi, viruses, plasmids, progenomes, rvdb}","description":"Type of database to be downloaded. [required]"},{"names":["--o-database"],"argument":"ARTIFACT","description":"Kaiju database. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fetch-ncbi-taxonomy","description":"Fetch NCBI reference taxonomy","usage":"qiime moshpit fetch-ncbi-taxonomy [OPTIONS]","options":[{"names":["--o-taxonomy"],"argument":"ARTIFACT","description":"NCBI reference taxonomy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-derep-mags","description":"Filter dereplicated MAGs.","usage":"qiime moshpit filter-derep-mags [OPTIONS]","options":[{"names":["--i-mags"],"argument":"ARTIFACT","description":"Dereplicated MAGs to filter. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata indicating which MAG ids to filter. [required]"},{"names":["--p-where"],"argument":"TEXT","description":"Optional SQLite WHERE clause specifying MAG metadata criteria that must be met to be included in the filtered data. If not provided, all MAGs in `metadata` that are also in the MAG data will be retained."},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"Defaults to False. If True, the MAGs selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]"},{"names":["--o-filtered-mags"],"argument":"ARTIFACT","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-mags","description":"Filter MAGs.","usage":"qiime moshpit filter-mags [OPTIONS]","options":[{"names":["--i-mags"],"argument":"ARTIFACT","description":"MAGs to filter. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata indicating which MAG ids to filter. [required]"},{"names":["--p-where"],"argument":"TEXT","description":"Optional SQLite WHERE clause specifying MAG metadata criteria that must be met to be included in the filtered data. If not provided, all MAGs in `metadata` that are also in the MAG data will be retained."},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"Defaults to False. If True, the MAGs selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]"},{"names":["--p-on"],"argument":"TEXT Choices('sample', 'mag')","description":"Whether to filter based on sample or MAG metadata."},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"(multiple Sample metadata indicating which MAG ids to filter."},{"names":["--o-filtered-mags"],"argument":"ARTIFACT","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-feature-lengths","description":"Get feature lengths.","usage":"qiime moshpit get-feature-lengths [OPTIONS]","options":[{"names":["--i-features"],"argument":"ARTIFACT","description":"Features to get lengths for. [required]"},{"names":["--o-lengths"],"argument":"ARTIFACT","description":"Feature lengths. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"inspect-kraken2-db","description":"Inspect a Kraken 2 database.","usage":"qiime moshpit inspect-kraken2-db [OPTIONS]","options":[{"names":["--i-db"],"argument":"ARTIFACT","description":"The Kraken 2 database for which to generate the report. [required]"},{"names":["--p-threads"],"argument":"INTEGER","description":"The number of threads to use.   Range(1, None) [default: 1]"},{"names":["--o-report"],"argument":"ARTIFACT","description":"The report of the supplied database. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"kraken2-to-features","description":"Select downstream features from Kraken 2","usage":"qiime moshpit kraken2-to-features [OPTIONS]","options":[{"names":["--i-reports"],"argument":"ARTIFACT","description":"Per-sample Kraken 2 reports. [required]"},{"names":["--p-coverage-threshold"],"argument":"NUMBER","description":"The minimum percent coverage required to produce a feature. [default: 0.1]"},{"names":["--o-table"],"argument":"ARTIFACT","description":"A presence/absence table of selected features. The features are not of even ranks, but will be the most specific rank available. [required]"},{"names":["--o-taxonomy"],"argument":"ARTIFACT","description":"Infra-clade ranks are ignored unless they are strain-level. Missing internal ranks are annotated by their next most specific rank, with the exception of k__Bacteria and k__Archaea which match their domain's name. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"kraken2-to-mag-features","description":"Select downstream MAG features from Kraken 2","usage":"qiime moshpit kraken2-to-mag-features [OPTIONS]","options":[{"names":["--i-reports"],"argument":"ARTIFACT","description":"Per-sample Kraken 2 reports. [required]"},{"names":["--i-hits"],"argument":"ARTIFACT","description":"Per-sample Kraken 2 output files. [required]"},{"names":["--p-coverage-threshold"],"argument":"NUMBER","description":"The minimum percent coverage required to produce a feature. [default: 0.1]"},{"names":["--o-taxonomy"],"argument":"ARTIFACT","description":"Infra-clade ranks are ignored unless they are strain-level. Missing internal ranks are annotated by their next most specific rank, with the exception of k__Bacteria and k__Archaea which match their domain's name. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partition-feature-data-mags","description":"Partition MAGs","usage":"qiime moshpit partition-feature-data-mags [OPTIONS]","options":[{"names":["--i-mags"],"argument":"ARTIFACT","description":"MAGs to partition. [required]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the MAGs into."},{"names":["--o-partitioned-mags"],"argument":"ARTIFACTS...","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partition-orthologs","description":"Partition orthologs","usage":"qiime moshpit partition-orthologs [OPTIONS]","options":[{"names":["--i-orthologs"],"argument":"ARTIFACT","description":"The orthologs to partition. [required]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the MAGs into."},{"names":["--o-partitioned-orthologs"],"argument":"ARTIFACTS...","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partition-sample-data-mags","description":"Partition MAGs","usage":"qiime moshpit partition-sample-data-mags [OPTIONS]","options":[{"names":["--i-mags"],"argument":"ARTIFACT","description":"The MAGs to partition. [required]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"Range(1, None) The number of partitions to split the MAGs into."},{"names":["--o-partitioned-mags"],"argument":"ARTIFACTS...","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"predict-genes-prodigal","description":"Predict gene sequences from MAGs using Prodigal.","usage":"qiime moshpit predict-genes-prodigal [OPTIONS]","options":[{"names":["--i-mags"],"argument":"ARTIFACT","description":"MAGs for which one wishes to predict genes. [required]"},{"names":["--p-translation-table-number"],"argument":"TEXT","description":"Translation table to be used to translate genes into a sequence of amino acids.."},{"names":["--o-loci"],"argument":"ARTIFACT","description":"Gene coordinates files (one per MAG) listing the location of each predicted gene as well as some additional scoring information. [required]"},{"names":["--o-genes"],"argument":"ARTIFACT","description":"Fasta files (one per MAG) with the nucleotide sequences of the predicted genes. [required]"},{"names":["--o-proteins"],"argument":"ARTIFACT GenomeData[Proteins]","description":"Fasta files (one per MAG) with the protein translation of the predicted genes. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"phylogeny","description":"Plugin for generating and manipulating phylogenies.","usage":"qiime phylogeny [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"align-to-tree-mafft-fasttree","description":"Build a phylogenetic tree using fasttree and","usage":"qiime phylogeny align-to-tree-mafft-fasttree [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to be used for creating a fasttree based rooted phylogenetic tree. [required]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads. (Use `auto` to automatically use all available cores) This value is used when aligning the sequences and creating the tree with fasttree. [default: 1]"},{"names":["--p-mask-max-gap-frequency"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences."},{"names":["--p-mask-min-conservation"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences."},{"names":["--p-parttree","--p-no-parttree"],"argument":"","description":"This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. [default: False]"},{"names":["--o-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The aligned sequences. [required]"},{"names":["--o-masked-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The masked alignment. [required]"},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The unrooted phylogenetic tree."},{"names":["--o-rooted-tree"],"argument":"ARTIFACT","description":"Phylogeny[Rooted] The rooted phylogenetic tree. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"align-to-tree-mafft-iqtree","description":"Build a phylogenetic tree using iqtree and","usage":"qiime phylogeny align-to-tree-mafft-iqtree [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads. (Use 0 to automatically use all available cores This value is used when aligning the sequences and creating the tree with iqtree."},{"names":["--p-mask-max-gap-frequency"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences."},{"names":["--p-mask-min-conservation"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences."},{"names":["--p-substitution-model"],"argument":"TEXT","description":"Model of Nucleotide Substitution. If not provided, IQ-TREE will determine the best fit substitution model automatically."},{"names":["--p-fast","--p-no-fast"],"argument":"","description":"Fast search to resemble FastTree. [default: False]"},{"names":["--p-alrt"],"argument":"INTEGER","description":"Single branch test method. Number of bootstrap replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is required."},{"names":["--p-stop-iter"],"argument":"INTEGER","description":"Number of unsuccessful iterations to stop. If not set, program defaults will be used."},{"names":["--p-perturb-nni-strength"],"argument":"NUMBER","description":"Perturbation strength for randomized NNI."},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed for the iqtree parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]"},{"names":["--o-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The aligned sequences. [required]"},{"names":["--o-masked-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The masked alignment. [required]"},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The unrooted phylogenetic tree."},{"names":["--o-rooted-tree"],"argument":"ARTIFACT","description":"Phylogeny[Rooted] The rooted phylogenetic tree. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"align-to-tree-mafft-raxml","description":"Build a phylogenetic tree using raxml and","usage":"qiime phylogeny align-to-tree-mafft-raxml [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads. (Use `all` to automatically use all available cores. This value is used when aligning the sequences and creating the tree with iqtree. [default: 1]"},{"names":["--p-mask-max-gap-frequency"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences."},{"names":["--p-mask-min-conservation"],"argument":"PROPORTION Range(0, 1, inclusive_end=True)","description":"The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences."},{"names":["--p-parttree","--p-no-parttree"],"argument":"","description":"This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. NOTE: if using this option, it is recomended that only the CAT-based substitution models of RAxML be considered for this pipeline."},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."},{"names":["--p-raxml-version"],"argument":"TEXT Choices('Standard', 'SSE3', 'AVX2')","description":"Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version."},{"names":["--o-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The aligned sequences. [required]"},{"names":["--o-masked-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"The masked alignment. [required]"},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The unrooted phylogenetic tree."},{"names":["--o-rooted-tree"],"argument":"ARTIFACT","description":"Phylogeny[Rooted] The rooted phylogenetic tree. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fasttree","description":"Construct a phylogenetic tree with FastTree.","usage":"qiime phylogeny fasttree [OPTIONS]","options":[{"names":["--i-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned sequences to be used for phylogenetic reconstruction. [required]"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads. Using more than one thread runs the non-deterministic variant of `FastTree` (`FastTreeMP`), and may result in a different tree than single-threading. See http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto` to automatically use all available cores) [default: 1]"},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The resulting phylogenetic tree."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-table","description":"Remove features from table if they're not","usage":"qiime phylogeny filter-table [OPTIONS]","options":[{"names":["--i-tree"],"argument":"ARTIFACT Phylogeny[Rooted | Unrooted]","description":"Tree where tip identifiers are the feature identifiers that should be retained in the table. [required]"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable","description":"Feature table that features should be filtered from."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-tree","description":"Remove features from tree based on metadata","usage":"qiime phylogeny filter-tree [OPTIONS]","options":[{"names":["--i-tree"],"argument":"ARTIFACT Phylogeny[Rooted¹ | Unrooted²]","description":"Tree that should be filtered [required]"},{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table which contains the identifier that should be retained in the tree"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Feature metadata to use with the 'where' statement or to select tips to be retained."},{"names":["--p-where"],"argument":"TEXT","description":"SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. [optional]"},{"names":["--o-filtered-tree"],"argument":"ARTIFACT Phylogeny[Rooted¹ | Unrooted²]","description":"The resulting phylogenetic tree. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"iqtree","description":"Construct a phylogenetic tree with IQ-TREE.","usage":"qiime phylogeny iqtree [OPTIONS]","options":[{"names":["--i-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned sequences to be used for phylogenetic reconstruction. [required]"},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed. If not set, program defaults"},{"names":["--p-n-cores"],"argument":"NTHREADS","description":"The number of cores to use for parallel processing."},{"names":["--p-n-cores-max"],"argument":"NTHREADS","description":"Limits the maximum number of cores to be used when"},{"names":["--p-n-runs"],"argument":"INTEGER","description":"Number of indepedent runs. Multiple independent"},{"names":["--p-substitution-model"],"argument":"TEXT","description":"Model of Nucleotide Substitution."},{"names":["--p-n-init-pars-trees"],"argument":"INTEGER","description":"Number of initial parsimony trees."},{"names":["--p-n-top-init-trees"],"argument":"INTEGER","description":"Number of top initial trees."},{"names":["--p-n-best-retain-trees"],"argument":"INTEGER","description":"Number of best trees retained during search."},{"names":["--p-n-iter"],"argument":"INTEGER","description":"Fix number of iterations to stop."},{"names":["--p-stop-iter"],"argument":"INTEGER","description":"Number of unsuccessful iterations to stop."},{"names":["--p-perturb-nni-strength"],"argument":"NUMBER","description":"Perturbation strength for randomized NNI."},{"names":["--p-spr-radius"],"argument":"INTEGER","description":"Radius for parsimony SPR search."},{"names":["--p-allnni","--p-no-allnni"],"argument":"","description":"Perform more thorough NNI search. [default: False]"},{"names":["--p-fast","--p-no-fast"],"argument":"","description":"Fast search to resemble FastTree. [default: False]"},{"names":["--p-alrt"],"argument":"INTEGER","description":"Single branch test method. Number of bootstrap"},{"names":["--p-abayes","--p-no-abayes"],"argument":"","description":"Single branch test method. Approximate Bayes test."},{"names":["--p-lbp"],"argument":"INTEGER","description":"Single branch test method. Number of bootstrap"},{"names":["--p-safe","--p-no-safe"],"argument":"","description":"Safe likelihood kernel to avoid numerical"},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The resulting phylogenetic tree."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"iqtree-ultrafast-bootstrap","description":"Construct a phylogenetic tree with IQ-TREE","usage":"qiime phylogeny iqtree-ultrafast-bootstrap [OPTIONS]","options":[{"names":["--i-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned sequences to be used for phylogenetic reconstruction. [required]"},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed. If not set, program defaults"},{"names":["--p-n-cores"],"argument":"NTHREADS","description":"The number of cores to use for parallel processing."},{"names":["--p-n-cores-max"],"argument":"NTHREADS","description":"Limits the maximum number of cores to be used when"},{"names":["--p-n-runs"],"argument":"INTEGER","description":"Number of indepedent runs. Multiple independent"},{"names":["--p-substitution-model"],"argument":"TEXT","description":"Model of Nucleotide Substitution."},{"names":["--p-bootstrap-replicates"],"argument":"INTEGER","description":"The number of bootstrap searches to perform."},{"names":["--p-n-init-pars-trees"],"argument":"INTEGER","description":"Number of initial parsimony trees."},{"names":["--p-n-top-init-trees"],"argument":"INTEGER","description":"Number of top initial trees."},{"names":["--p-n-best-retain-trees"],"argument":"INTEGER","description":"Number of best trees retained during search."},{"names":["--p-stop-iter"],"argument":"INTEGER","description":"Number of unsuccessful iterations to stop."},{"names":["--p-perturb-nni-strength"],"argument":"NUMBER","description":"Perturbation strength for randomized NNI."},{"names":["--p-spr-radius"],"argument":"INTEGER","description":"Radius for parsimony SPR search."},{"names":["--p-n-max-ufboot-iter"],"argument":"INTEGER","description":"Maximum number of iterations."},{"names":["--p-n-ufboot-steps"],"argument":"INTEGER","description":"Number of iterations for UFBoot stopping rule."},{"names":["--p-min-cor-ufboot"],"argument":"NUMBER","description":"Minimum correlation coefficient."},{"names":["--p-ep-break-ufboot"],"argument":"NUMBER","description":"Epsilon value to break tie."},{"names":["--p-allnni","--p-no-allnni"],"argument":"","description":"Perform more thorough NNI search. [default: False]"},{"names":["--p-alrt"],"argument":"INTEGER","description":"Single branch test method."},{"names":["--p-abayes","--p-no-abayes"],"argument":"","description":"Single branch test method."},{"names":["--p-lbp"],"argument":"INTEGER","description":"Single branch test method."},{"names":["--p-bnni","--p-no-bnni"],"argument":"","description":"Optimize UFBoot trees by NNI on bootstrap alignment."},{"names":["--p-safe","--p-no-safe"],"argument":"","description":"Safe likelihood kernel to avoid numerical underflow."},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The resulting phylogenetic tree."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"midpoint-root","description":"Midpoint root an unrooted phylogenetic tree.","usage":"qiime phylogeny midpoint-root [OPTIONS]","options":[{"names":["--i-tree"],"argument":"ARTIFACT Phylogeny[Unrooted]","description":"The phylogenetic tree to be rooted. [required]"},{"names":["--o-rooted-tree"],"argument":"ARTIFACT","description":"Phylogeny[Rooted] The rooted phylogenetic tree. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"raxml","description":"Construct a phylogenetic tree with RAxML.","usage":"qiime phylogeny raxml [OPTIONS]","options":[{"names":["--i-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned sequences to be used for phylogenetic reconstruction. [required]"},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."},{"names":["--p-n-searches"],"argument":"INTEGER","description":"The number of independent maximum likelihood"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML. [default: 1]"},{"names":["--p-raxml-version"],"argument":"TEXT Choices('Standard', 'SSE3', 'AVX2')","description":"Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version."},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The resulting phylogenetic tree."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"raxml-rapid-bootstrap","description":"Construct a phylogenetic tree with bootstrap","usage":"qiime phylogeny raxml-rapid-bootstrap [OPTIONS]","options":[{"names":["--i-alignment"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned sequences to be used for phylogenetic reconstruction. [required]"},{"names":["--p-seed"],"argument":"INTEGER","description":"Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."},{"names":["--p-rapid-bootstrap-seed"],"argument":"INTEGER","description":"Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen."},{"names":["--p-bootstrap-replicates"],"argument":"","description":"INTEGER"},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML. [default: 1]"},{"names":["--p-raxml-version"],"argument":"TEXT Choices('Standard', 'SSE3', 'AVX2')","description":"Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version."},{"names":["--o-tree"],"argument":"ARTIFACT","description":"The resulting phylogenetic tree."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"robinson-foulds","description":"Calculate Robinson-Foulds distance between","usage":"qiime phylogeny robinson-foulds [OPTIONS]","options":[{"names":["--i-trees"],"argument":"ARTIFACTS... List[Phylogeny[Rooted | Unrooted]]","description":"Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric. [required]"},{"names":["--p-labels"],"argument":"TEXT...","description":"Labels to use for the tree names in the distance"},{"names":["--p-missing-tips"],"argument":"TEXT Choices('error', 'intersect-all')","description":"How to handle tips that are not shared between trees. \"error\" will raise an error if the set of tips is not identical between all input trees. \"intersect-all\" will remove tips that are not shared between all trees before computing distances beteen trees. [default: 'error']"},{"names":["--o-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix The distances between trees as a symmetric matrix."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"quality-control","description":"Plugin for quality control of feature and sequence data.","usage":"qiime quality-control [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"bowtie2-build","description":"Build bowtie2 index from reference sequences.","usage":"qiime quality-control bowtie2-build [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences used to build bowtie2 index."},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"Number of threads to launch.   [default: 1]"},{"names":["--o-database"],"argument":"ARTIFACT","description":"Bowtie2 index."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"decontam-identify","description":"Identify contaminants","usage":"qiime quality-control decontam-identify [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table which contaminate sequences will be identified from [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter [required]"},{"names":["--p-method"],"argument":"TEXT Choices('combined', 'frequency', 'prevalence')","description":"Select how to which method to id contaminants with; Prevalence: Utilizes control ASVs/OTUs to identify contaminants, Frequency: Utilizes sample concentration information to identify contaminants, Combined: Utilizes both Prevalence and Frequency methods when identifying contaminants [default: 'prevalence']"},{"names":["--p-freq-concentration-column"],"argument":"TEXT","description":"Input column name that has concentration information for the samples [optional]"},{"names":["--p-prev-control-column"],"argument":"TEXT","description":"Input column name containing experimental or control sample metadata [optional]"},{"names":["--p-prev-control-indicator"],"argument":"TEXT","description":"indicate the control sample identifier (e.g. \"control\" or \"blank\") [optional]"},{"names":["--o-decontam-scores"],"argument":"ARTIFACT FeatureData[DecontamScore]","description":"The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"decontam-identify-batches","description":"Identify contaminants in Batch Mode","usage":"qiime quality-control decontam-identify-batches [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table which contaminate sequences will be identified from [required]"},{"names":["--i-rep-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Representative Sequences table which contaminate seqeunces will be removed from [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter [required]"},{"names":["--p-split-column"],"argument":"TEXT","description":"input metadata columns that you wish to subset the ASV table byNote: Column names must be in quotes and delimited by a space [required]"},{"names":["--p-method"],"argument":"TEXT Choices('combined', 'frequency', 'prevalence')","description":"Select how to which method to id contaminants with; Prevalence: Utilizes control ASVs/OTUs to identify contaminants, Frequency: Utilizes sample concentration information to identify contaminants, Combined: Utilizes both Prevalence and Frequency methods when identifying contaminants [required]"},{"names":["--p-filter-empty-features","--p-no-filter-empty-features"],"argument":"","description":"If true, features which are not present in a split feature table are dropped. [optional]"},{"names":["--p-freq-concentration-column"],"argument":"TEXT","description":"Input column name that has concentration information for the samples [optional]"},{"names":["--p-prev-control-column"],"argument":"TEXT","description":"Input column name containing experimental or control sample metadata [optional]"},{"names":["--p-prev-control-indicator"],"argument":"TEXT","description":"indicate the control sample identifier (e.g. \"control\" or \"blank\") [optional]"},{"names":["--p-threshold"],"argument":"NUMBER","description":"Select threshold cutoff for decontam algorithm scores [default: 0.1]"},{"names":["--p-weighted","--p-no-weighted"],"argument":"","description":"weight the decontam scores by their associated read number [default: True]"},{"names":["--p-bin-size"],"argument":"NUMBER","description":"Select bin size for the histogram [default: 0.02]"},{"names":["--o-batch-subset-tables"],"argument":"ARTIFACTS... Collection[FeatureTable[Frequency]]","description":"Directory where feature tables split based on metadata and parameter split-column values should be written. [required]"},{"names":["--o-decontam-scores"],"argument":"ARTIFACTS... Collection[FeatureData[DecontamScore]]","description":"The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence [required]"},{"names":["--o-score-histograms"],"argument":"VISUALIZATION","description":"The vizulaizer histograms for all decontam score objects generated from the pipeline [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"decontam-remove","description":"Remove contaminants","usage":"qiime quality-control decontam-remove [OPTIONS]","options":[{"names":["--i-decontam-scores"],"argument":"ARTIFACT FeatureData[DecontamScore]","description":"Pre-feature decontam scores. [required]"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table from which contaminants will be removed. [required]"},{"names":["--i-rep-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Feature representative sequences from which contaminants will be removed. [required]"},{"names":["--p-threshold"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Decontam score threshold. Features with a score less than or equal to this threshold will be removed."},{"names":["--o-filtered-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table with contaminants removed. [required]"},{"names":["--o-filtered-rep-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Feature representative sequences with contaminants removed. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"decontam-score-viz","description":"Generate a histogram representation of the scores","usage":"qiime quality-control decontam-score-viz [OPTIONS]","options":[{"names":["--i-decontam-scores"],"argument":"ARTIFACTS... Collection[FeatureData[DecontamScore]]","description":"Output from decontam identify to be visualized"},{"names":["--i-table"],"argument":"ARTIFACTS... Collection[FeatureTable[Frequency]]","description":"Raw OTU/ASV table that was used as input to decontam-identify [required]"},{"names":["--i-rep-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Representative Sequences table which contaminate sequences will be removed from [optional]"},{"names":["--p-threshold"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Select threshold cutoff for decontam algorithm scores [default: 0.1]"},{"names":["--p-weighted","--p-no-weighted"],"argument":"","description":"weight the decontam scores by their associated read number [default: True]"},{"names":["--p-bin-size"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Select bin size for the histogram [default: 0.02]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-composition","description":"Evaluate expected vs. observed taxonomic composition of samples","usage":"qiime quality-control evaluate-composition [OPTIONS]","options":[{"names":["--i-expected-features"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Expected feature compositions [required]"},{"names":["--i-observed-features"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Observed feature compositions [required]"},{"names":["--p-depth"],"argument":"INTEGER","description":"Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [default: 7]"},{"names":["--p-plot-tar","--p-no-plot-tar"],"argument":"","description":"Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true positive features divided by the total number of observed features (TAR = true positives / (true positives + false positives)). [default: True]"},{"names":["--p-plot-tdr","--p-no-plot-tdr"],"argument":"","description":"Plot taxon detection rate (TDR) on score plot. TDR is the number of true positive features divided by the total number of expected features (TDR = true positives / (true positives + false negatives)). [default: True]"},{"names":["--p-plot-r-value","--p-no-plot-r-value"],"argument":"","description":"Plot expected vs. observed linear regression r value on score plot. [default: False]"},{"names":["--p-plot-r-squared","--p-no-plot-r-squared"],"argument":"","description":"Plot expected vs. observed linear regression r-squared value on score plot. [default: True]"},{"names":["--p-plot-bray-curtis","--p-no-plot-bray-curtis"],"argument":"","description":"Plot expected vs. observed Bray-Curtis dissimilarity scores on score plot. [default: False]"},{"names":["--p-plot-jaccard","--p-no-plot-jaccard"],"argument":"","description":"Plot expected vs. observed Jaccard distances scores on score plot. [default: False]"},{"names":["--p-plot-observed-features","--p-no-plot-observed-features"],"argument":"","description":"Plot observed features count on score plot."},{"names":["--p-plot-observed-features-ratio","--p-no-plot-observed-features-ratio"],"argument":"","description":"Plot ratio of observed:expected features on score plot. [default: True]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs. [optional]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-seqs","description":"Compare query (observed) vs. reference (expected) sequences.","usage":"qiime quality-control evaluate-seqs [OPTIONS]","options":[{"names":["--i-query-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to test for exclusion [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences to align against feature sequences"},{"names":["--p-show-alignments","--p-no-show-alignments"],"argument":"","description":"Option to plot pairwise alignments of query sequences and their top hits. [default: False]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-taxonomy","description":"Evaluate expected vs. observed taxonomic assignments","usage":"qiime quality-control evaluate-taxonomy [OPTIONS]","options":[{"names":["--i-expected-taxa"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Expected taxonomic assignments [required]"},{"names":["--i-observed-taxa"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Observed taxonomic assignments [required]"},{"names":["--i-feature-table"],"argument":"ARTIFACT FeatureTable[RelativeFrequency]","description":"Optional feature table containing relative frequency of each feature, used to weight accuracy scores by frequency. Must contain all features found in expected and/or observed taxa. Features found in the table but not the expected/observed taxa will be dropped prior to analysis. [optional]"},{"names":["--p-depth"],"argument":"INTEGER","description":"Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [required]"},{"names":["--p-require-exp-ids","--p-no-require-exp-ids"],"argument":"","description":"Require that all features found in observed taxa must be found in expected taxa or raise error."},{"names":["--p-require-obs-ids","--p-no-require-obs-ids"],"argument":"","description":"Require that all features found in expected taxa must be found in observed taxa or raise error."},{"names":["--p-sample-id"],"argument":"TEXT","description":"Optional sample ID to use for extracting frequency data from feature table, and for labeling accuracy results. If no sample-id is provided, feature frequencies are derived from the sum of all samples present in the feature table. [optional]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"exclude-seqs","description":"Exclude sequences by alignment","usage":"qiime quality-control exclude-seqs [OPTIONS]","options":[{"names":["--i-query-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to test for exclusion [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences to align against feature sequences [required]"},{"names":["--p-perc-identity"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0] [default: 0.97]"},{"names":["--p-evalue"],"argument":"NUMBER","description":"BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default. [optional]"},{"names":["--p-perc-query-aligned"],"argument":"NUMBER","description":"Percent of query sequence that must align to reference in order to be accepted as a hit."},{"names":["--p-threads"],"argument":"NTHREADS","description":"Number of threads to use. Only applies to vsearch method. [default: 1]"},{"names":["--o-sequence-hits"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Subset of feature sequences that align to reference sequences [required]"},{"names":["--o-sequence-misses"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Subset of feature sequences that do not align to reference sequences [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-reads","description":"Filter demultiplexed sequences by alignment to reference database.","usage":"qiime quality-control filter-reads [OPTIONS]","options":[{"names":["--i-database"],"argument":"ARTIFACT","description":"Bowtie2 indexed database."},{"names":["--p-n-threads"],"argument":"NTHREADS","description":"Number of alignment threads to launch. [default: 1]"},{"names":["--p-mode"],"argument":"TEXT Choices('local', 'global')","description":"Bowtie2 alignment settings. See bowtie2 manual for more details. [default: 'local']"},{"names":["--p-ref-gap-open-penalty"],"argument":"","description":"INTEGER"},{"names":["--p-ref-gap-ext-penalty"],"argument":"","description":"INTEGER"},{"names":["--p-exclude-seqs","--p-no-exclude-seqs"],"argument":"","description":"Exclude sequences that align to reference. Set this option to False to exclude sequences that do not align to the reference database. [default: True]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"quality-filter","description":"Plugin for PHRED-based filtering and trimming.","usage":"qiime quality-filter [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"rescript","description":"Pipeline for reference sequence annotation and curation.","usage":"qiime rescript [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"cull-seqs","description":"Removes sequences that contain at least the specified number of degenerate bases and/or homopolymers of a given length.","usage":"qiime rescript cull-seqs [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence | RNASequence]","description":"DNA or RNA Sequences to be screened for removal based on degenerate base and homopolymer screening criteria. [required]"},{"names":["--p-num-degenerates"],"argument":"INTEGER","description":"Sequences with N, or more, degenerate bases will be removed."},{"names":["--p-homopolymer-length"],"argument":"INTEGER","description":"Sequences containing a homopolymer sequence of length N, or greater, will be removed."},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of concurrent processes to use while processing sequences."},{"names":["--o-clean-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting DNA sequences that pass degenerate base and homopolymer screening criteria. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"degap-seqs","description":"Remove gaps from DNA sequence alignments.","usage":"qiime rescript degap-seqs [OPTIONS]","options":[{"names":["--i-aligned-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned DNA Sequences to be degapped. [required]"},{"names":["--p-min-length"],"argument":"INTEGER","description":"Minimum length of sequence to be returned after degapping. [default: 1]"},{"names":["--o-degapped-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The resulting unaligned (degapped) DNA sequences."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"dereplicate","description":"Dereplicate features with matching sequences and taxonomies.","usage":"qiime rescript dereplicate [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to be dereplicated [required]"},{"names":["--i-taxa"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic classifications of sequences to be dereplicated [required]"},{"names":["--p-mode"],"argument":"TEXT Choices('uniq', 'lca', 'majority', 'super')","description":"How to handle dereplication when sequences map to distinct taxonomies. \"uniq\" will retain all sequences with unique taxonomic affiliations. \"lca\" will find the least common ancestor among all taxa sharing a sequence. \"majority\" will find the most common taxonomic label associated with that sequence; note that in the event of a tie, \"majority\" will pick the winner arbitrarily. \"super\" finds the LCA consensus while giving preference to majority labels and collapsing substrings into superstrings. For example, when a more specific taxonomy does not contradict a less specific taxonomy, the more specific is chosen. That is, \"g__Faecalibacterium; s__prausnitzii\", will be preferred over \"g__Faecalibacterium; s__\""},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of computation threads to use (1 to 256)."},{"names":["--p-rank-handles"],"argument":"VALUES...","description":"Specifies the set of rank handles used to backfill missing ranks in the resulting dereplicated taxonomy."},{"names":["--p-derep-prefix","--p-no-derep-prefix"],"argument":"","description":"Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False]"},{"names":["--o-dereplicated-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"[required]"},{"names":["--o-dereplicated-taxa"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"edit-taxonomy","description":"Edit taxonomy strings with find and replace terms.","usage":"qiime rescript edit-taxonomy [OPTIONS]","options":[{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomy strings data to be edited. [required]"},{"names":["--m-replacement-map-file"],"argument":"","description":"METADATA"},{"names":["--m-replacement-map-column"],"argument":"COLUMN  MetadataColumn[Categorical]","description":"A tab-delimitad metadata file in which the strings in the 'id' column are replaced by the 'replacement-strings' in the second column. All strings in the 'id' column must be unique! [optional]"},{"names":["--p-search-strings"],"argument":"TEXT...","description":"Only used in conjuntion with 'replacement-strings'."},{"names":["--p-replacement-strings"],"argument":"TEXT...","description":"Only used in conjuntion with 'search-strings'."},{"names":["--p-use-regex","--p-no-use-regex"],"argument":"","description":"Toggle regular expressions. By default, only litereal substring matching is performed."},{"names":["--o-edited-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomy in which the original strings are replaced by user-supplied strings. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-classifications","description":"Interactively evaluate taxonomic classification accuracy.","usage":"qiime rescript evaluate-classifications [OPTIONS]","options":[{"names":["--i-expected-taxonomies"],"argument":"ARTIFACTS... List[FeatureData[Taxonomy]]","description":"True taxonomic labels for one more more sets of features. [required]"},{"names":["--i-observed-taxonomies"],"argument":"ARTIFACTS... List[FeatureData[Taxonomy]]","description":"Predicted classifications of same sets of features, input in same order as expected-taxonomies."},{"names":["--p-labels"],"argument":"TEXT...","description":"List of labels to use for labeling evaluation"},{"names":["--o-evaluation"],"argument":"VISUALIZATION","description":"Visualization of classification accuracy results."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-cross-validate","description":"Evaluate DNA sequence reference database via cross-validated taxonomic classification.","usage":"qiime rescript evaluate-cross-validate [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences to use for classifier training/testing. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Reference taxonomy to use for classifier training/testing. [required]"},{"names":["--p-k"],"argument":"INTEGER","description":"Number of stratified folds."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by the random number generator."},{"names":["--p-reads-per-batch"],"argument":"VALUE","description":"Number of reads to process in each batch. If \"auto\", this parameter is autoscaled to min( number of query sequences / n-jobs, 20000)."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]"},{"names":["--p-confidence"],"argument":"VALUE","description":"Confidence threshold for limiting taxonomic depth."},{"names":["--o-expected-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Expected taxonomic label for each input sequence. Taxonomic labels may be truncated due to k-fold CV and stratification. [required]"},{"names":["--o-observed-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Observed taxonomic label for each input sequence, predicted by cross-validation. [required]"},{"names":["--o-evaluation"],"argument":"VISUALIZATION","description":"Visualization of cross-validated accuracy results. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-fit-classifier","description":"Evaluate and train naive Bayes classifier on reference sequences.","usage":"qiime rescript evaluate-fit-classifier [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences to use for classifier training/testing. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Reference taxonomy to use for classifier training/testing. [required]"},{"names":["--p-reads-per-batch"],"argument":"VALUE","description":"Number of reads to process in each batch. If \"auto\", this parameter is autoscaled to min( number of query sequences / n-jobs, 20000)."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]"},{"names":["--p-confidence"],"argument":"VALUE","description":"Confidence threshold for limiting taxonomic depth."},{"names":["--o-classifier"],"argument":"ARTIFACT","description":"Trained naive Bayes taxonomic classifier. [required]"},{"names":["--o-evaluation"],"argument":"VISUALIZATION","description":"Visualization of classification accuracy results. [required]"},{"names":["--o-observed-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Observed taxonomic label for each input sequence, predicted by the trained classifier. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-seqs","description":"Compute summary statistics on sequence artifact(s).","usage":"qiime rescript evaluate-seqs [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACTS... List[FeatureData[Sequence]]","description":"One or more sets of sequences to evaluate. [required]"},{"names":["--p-labels"],"argument":"TEXT...","description":"List of labels to use for labeling evaluation results in the resulting visualization."},{"names":["--p-kmer-lengths"],"argument":"INTEGERS...","description":"Sequence kmer lengths to optionally use for entropy calculation."},{"names":["--p-subsample-kmers"],"argument":"PROPORTION","description":"Optionally subsample sequences prior to kmer entropy measurement."},{"names":["--p-palette"],"argument":"TEXT","description":"Color palette to use for plotting evaluation results."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-taxonomy","description":"Compute summary statistics on taxonomy artifact(s).","usage":"qiime rescript evaluate-taxonomy [OPTIONS]","options":[{"names":["--i-taxonomies"],"argument":"ARTIFACTS... List[FeatureData[Taxonomy]]","description":"One or more taxonomies to evaluate. [required]"},{"names":["--p-labels"],"argument":"TEXT...","description":"List of labels to use for labeling evaluation results in the resulting visualization."},{"names":["--p-rank-handle-regex"],"argument":"TEXT","description":"Regular expression indicating which taxonomic rank a label belongs to; this handle is stripped from the label prior to operating on the taxonomy. The net effect is that ambiguous or empty levels can be removed prior to comparison, enabling selection of taxonomies with more complete taxonomic information. For example, \"^[dkpcofgs]__\" will recognize greengenes or silva rank handles. [optional]"},{"names":["--o-taxonomy-stats"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"extract-seq-segments","description":"Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value.","usage":"qiime rescript extract-seq-segments [OPTIONS]","options":[{"names":["--i-input-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences from which matching shorter sequence segments (regions) can be extracted from. Sequences containing segments that match those from 'reference-segment-sequences' will have those segments extracted and written to file. [required]"},{"names":["--i-reference-segment-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequence segments that will be used to search for and extract matching segments from 'sequences'. [required]"},{"names":["--p-perc-identity"],"argument":"PROPORTION","description":"The percent identity at which clustering should be performed."},{"names":["--p-min-seq-len"],"argument":"INTEGER","description":"Minimum length of sequence allowed for searching."},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of computation threads to use (1 to 256)."},{"names":["--o-extracted-sequence-segments"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Extracted sequence segments from 'input-sequences' that succesfully aligned to 'reference-segment-sequences'. [required]"},{"names":["--o-unmatched-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences in 'input-sequences' that did not have matching sequence segments within 'reference-segment-sequences'. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-seqs-length","description":"Filter sequences by length.","usage":"qiime rescript filter-seqs-length [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to be filtered by length. [required]"},{"names":["--p-global-min"],"argument":"INTEGER","description":"The minimum length threshold for filtering all sequences."},{"names":["--p-global-max"],"argument":"INTEGER","description":"The maximum length threshold for filtering all sequences."},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of computation threads to use (1 to 256)."},{"names":["--o-filtered-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences that pass the filtering thresholds."},{"names":["--o-discarded-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences that fall outside the filtering thresholds. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-seqs-length-by-taxon","description":"Filter sequences by length and taxonomic group.","usage":"qiime rescript filter-seqs-length-by-taxon [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to be filtered by length. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic classifications of sequences to be filtered. [required]"},{"names":["--p-labels"],"argument":"TEXT...","description":"One or more taxonomic labels to use for conditional filtering. [required]"},{"names":["--p-min-lens"],"argument":"INTEGERS...","description":"Minimum length thresholds to use for filtering sequences associated with each label."},{"names":["--p-max-lens"],"argument":"INTEGERS...","description":"Maximum length thresholds to use for filtering sequences associated with each label."},{"names":["--p-global-min"],"argument":"INTEGER","description":"The minimum length threshold for filtering all sequences."},{"names":["--p-global-max"],"argument":"INTEGER","description":"The maximum length threshold for filtering all sequences."},{"names":["--o-filtered-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences that pass the filtering thresholds."},{"names":["--o-discarded-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences that fall outside the filtering thresholds. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-taxa","description":"Filter taxonomy by list of IDs or search criteria.","usage":"qiime rescript filter-taxa [OPTIONS]","options":[{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomy to filter. [required]"},{"names":["--m-ids-to-keep-file"],"argument":"METADATA...","description":"List of IDs to keep (as Metadata)."},{"names":["--p-include"],"argument":"TEXT...","description":"List of search terms. Taxa containing one or more of these terms will be retained."},{"names":["--p-exclude"],"argument":"TEXT...","description":"List of search terms. Taxa containing one or more of these terms will be excluded."},{"names":["--o-filtered-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"The filtered taxonomy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-gtdb-data","description":"Download, parse, and import SSU GTDB reference data.","usage":"qiime rescript get-gtdb-data [OPTIONS]","options":[{"names":["--p-version"],"argument":"TEXT Choices('202.0', '207.0', '214.0', '214.1')","description":"GTDB database version to download. [default: '214.1']"},{"names":["--p-domain"],"argument":"TEXT Choices('Both', 'Bacteria', 'Archaea')","description":"SSU sequence and taxonomy data to download from a given microbial domain from GTDB. 'Both' will fetch both bacterial and archaeal data. 'Bacteria' will only fetch bacterial data. 'Archaea' will only fetch archaeal data. This only applies to 'db-type SpeciesReps'. [default: 'Both']"},{"names":["--p-db-type"],"argument":"TEXT Choices('All', 'SpeciesReps')","description":"'All': All SSU data that pass the quality-control of GTDB, but are not clustered into representative species. 'SpeciesReps': SSU gene sequences identified within the set of representative species. Note: if 'All' is used, the 'domain' parameter will be ignored as GTDB does not maintain separate domain-level files for these non-clustered data. [default: 'SpeciesReps']"},{"names":["--o-gtdb-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"SSU GTDB reference taxonomy. [required]"},{"names":["--o-gtdb-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"SSU GTDB reference sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-ncbi-data","description":"Download, parse, and import NCBI sequences and taxonomies","usage":"qiime rescript get-ncbi-data [OPTIONS]","options":[{"names":["--p-query"],"argument":"TEXT","description":"Query on the NCBI Nucleotide database [optional]"},{"names":["--m-accession-ids-file"],"argument":"METADATA...","description":"List of accession ids for sequences in the NCBI Nucleotide database."},{"names":["--p-ranks"],"argument":"TEXT...","description":"List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy database."},{"names":["--p-rank-propagation","--p-no-rank-propagation"],"argument":"","description":"Propagate known ranks to missing ranks if true"},{"names":["--p-logging-level"],"argument":"TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL')","description":"Logging level"},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of concurrent download connections. More is faster until you run out of bandwidth. [default: 1]"},{"names":["--o-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences from the NCBI Nucleotide database [required]"},{"names":["--o-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomies from the NCBI Taxonomy database [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-ncbi-data-protein","description":"Download, parse, and import NCBI protein sequences and taxonomies","usage":"qiime rescript get-ncbi-data-protein [OPTIONS]","options":[{"names":["--p-query"],"argument":"TEXT","description":"Query on the NCBI Protein database [optional]"},{"names":["--m-accession-ids-file"],"argument":"METADATA...","description":"List of accession ids for sequences in the NCBI Protein database."},{"names":["--p-ranks"],"argument":"TEXT...","description":"List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy database."},{"names":["--p-rank-propagation","--p-no-rank-propagation"],"argument":"","description":"Propagate known ranks to missing ranks if true"},{"names":["--p-n-jobs"],"argument":"INTEGER","description":"Number of concurrent download connections. More is faster until you run out of bandwidth. [default: 1]"},{"names":["--o-sequences"],"argument":"ARTIFACT FeatureData[ProteinSequence]","description":"Sequences from the NCBI Protein database [required]"},{"names":["--o-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomies from the NCBI Taxonomy database [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-ncbi-genomes","description":"Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.","usage":"qiime rescript get-ncbi-genomes [OPTIONS]","options":[{"names":["--p-taxon"],"argument":"TEXT","description":"NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank. [required]"},{"names":["--p-assembly-source"],"argument":"TEXT Choices('refseq', 'genbank')","description":"Fetch only RefSeq or GenBank genome assemblies."},{"names":["--p-assembly-levels"],"argument":"TEXT... Choices('complete_genome', 'chromosome', 'scaffold', 'contig')","description":"Fetch only genome assemblies that are one of the specified assembly levels."},{"names":["--p-only-reference","--p-no-only-reference"],"argument":"","description":"Fetch only reference and representative genome assemblies. [default: True]"},{"names":["--p-tax-exact-match","--p-no-tax-exact-match"],"argument":"","description":"If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too. [default: False]"},{"names":["--p-page-size"],"argument":"INTEGER Range(20, 1000, inclusive_end=True)","description":"The maximum number of genome assemblies to return per request. If number of genomes to fetch is higher than this number, requests will be repeated until all assemblies are fetched. [default: 20]"},{"names":["--o-genome-assemblies"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Nucleotide sequences of requested genomes. [required]"},{"names":["--o-loci"],"argument":"ARTIFACT","description":"Loci features of requested genomes."},{"names":["--o-proteins"],"argument":"ARTIFACT GenomeData[Proteins]","description":"Protein sequences originating from requested genomes. [required]"},{"names":["--o-taxonomies"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomies of requested genomes. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-silva-data","description":"Download, parse, and import SILVA database.","usage":"qiime rescript get-silva-data [OPTIONS]","options":[{"names":["--p-include-species-labels","--p-no-include-species-labels"],"argument":"","description":"Include species rank labels in taxonomy output. Note: species-labels may not be reliable in all cases. [default: False]"},{"names":["--p-rank-propagation","--p-no-rank-propagation"],"argument":"","description":"If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for 'f__Pasteurellaceae; g__'then the 'f__' rank will be propagated to become: 'f__Pasteurellaceae; g__Pasteurellaceae'."},{"names":["--p-download-sequences","--p-no-download-sequences"],"argument":"","description":"Toggle whether or not to download and import the SILVA reference sequences associated with the release. Skipping the sequences is useful if you only want to download and parse the taxonomy, e.g., a local copy of the sequences already exists or for testing purposes. NOTE: if this option is used, a `silva-sequences` output is still created, but contains no data. [default: True]"},{"names":["--o-silva-sequences"],"argument":"ARTIFACT FeatureData[RNASequence]","description":"SILVA reference sequences. [required]"},{"names":["--o-silva-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"SILVA reference taxonomy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-unite-data","description":"Download and import UNITE reference data.","usage":"qiime rescript get-unite-data [OPTIONS]","options":[{"names":["--p-version"],"argument":"TEXT Choices('10.0', '9.0', '8.3', '8.2')","description":"UNITE version to download. [default: '10.0']"},{"names":["--p-taxon-group"],"argument":"TEXT Choices('fungi', 'eukaryotes')","description":"Download a database with only 'fungi' or including all 'eukaryotes'. [default: 'eukaryotes']"},{"names":["--p-cluster-id"],"argument":"TEXT Choices('99', '97', 'dynamic')","description":"Percent similarity at which sequences in the of database were clustered. [default: '99']"},{"names":["--p-singletons","--p-no-singletons"],"argument":"","description":"Include singleton clusters in the database."},{"names":["--o-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"UNITE reference taxonomy. [required]"},{"names":["--o-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"UNITE reference sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"merge-taxa","description":"Compare taxonomies and select the longest, highest scoring, or find the least common ancestor.","usage":"qiime rescript merge-taxa [OPTIONS]","options":[{"names":["--i-data"],"argument":"ARTIFACTS... List[FeatureData[Taxonomy]]","description":"Two or more feature taxonomies to be merged."},{"names":["--p-mode"],"argument":"TEXT Choices('len', 'lca', 'score', 'super', 'majority')","description":"How to merge feature taxonomies: \"len\" will select the taxonomy with the most elements (e.g., species level will beat genus level); \"lca\" will find the least common ancestor and report this consensus taxonomy; \"score\" will select the taxonomy with the highest score (e.g., confidence or consensus score). Note that \"score\" assumes that this score is always contained as the second column in a feature taxonomy dataframe. \"majority\" finds the LCA consensus while giving preference to majority labels. \"super\" finds the LCA consensus while giving preference to majority labels and collapsing substrings into superstrings. For example, when a more specific taxonomy does not contradict a less specific taxonomy, the more specific is chosen. That is, \"g__Faecalibacterium; s__prausnitzii\", will be preferred over \"g__Faecalibacterium; s__\" [default: 'len']"},{"names":["--p-rank-handle-regex"],"argument":"TEXT","description":"Regular expression indicating which taxonomic rank a label belongs to; this handle is stripped from the label prior to operating on the taxonomy. The net effect is that ambiguous or empty levels can be removed prior to comparison, enabling selection of taxonomies with more complete taxonomic information. For example, \"^[dkpcofgs]__\" will recognize greengenes or silva rank handles. Note that rank_handles are removed but not replaced; use the new_rank_handle parameter to replace the rank handles. [default: '^[dkpcofgs]__']"},{"names":["--p-new-rank-handles"],"argument":"VALUES...","description":"Specifies the set of rank handles to prepend to taxonomic labels at each rank."},{"names":["--p-unclassified-label"],"argument":"TEXT","description":"Specifies what label should be used for taxonomies that could not be resolved (when LCA modes are used)."},{"names":["--o-merged-data"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"orient-seqs","description":"Orient input sequences by comparison against reference.","usage":"qiime rescript orient-seqs [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences to be oriented. [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Reference sequences to orient against. If no reference is provided, all the sequences will be reverse complemented and all parameters will be ignored. [optional]"},{"names":["--p-threads"],"argument":"INTEGER","description":"Number of computation threads to use (1 to 256)."},{"names":["--p-dbmask"],"argument":"TEXT Choices('none', 'dust', 'soft')","description":"Mask regions in the target database sequences using the dust method, or do not mask (none). When using soft masking, search commands become case sensitive."},{"names":["--p-relabel"],"argument":"TEXT","description":"Relabel sequences using the prefix string and a ticker (1, 2, 3, etc.) to construct the new headers. Use --sizeout to conserve the abundance annotations."},{"names":["--p-relabel-keep","--p-no-relabel-keep"],"argument":"","description":"When relabeling, keep the original identifier in the header after a space. [optional]"},{"names":["--p-relabel-md5","--p-no-relabel-md5"],"argument":"","description":"When relabeling, use the MD5 digest of the sequence as the new identifier. Use --sizeout to conserve the abundance annotations. [optional]"},{"names":["--p-relabel-self","--p-no-relabel-self"],"argument":"","description":"Relabel sequences using the sequence itself as a label. [optional]"},{"names":["--p-relabel-sha1","--p-no-relabel-sha1"],"argument":"","description":"When relabeling, use the SHA1 digest of the sequence as the new identifier. The probability of a collision is smaller than the MD5 algorithm."},{"names":["--p-sizein","--p-no-sizein"],"argument":"","description":"In de novo mode, abundance annotations (pattern `[>;]size=integer[;]`) present in sequence headers are taken into account. [optional]"},{"names":["--p-sizeout","--p-no-sizeout"],"argument":"","description":"Add abundance annotations to the output FASTA files. [optional]"},{"names":["--o-oriented-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query sequences in same orientation as top matching reference sequence. [required]"},{"names":["--o-unmatched-seqs"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Query sequences that fail to match at least one reference sequence in either + or - orientation. This will be empty if no refrence is provided."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"parse-silva-taxonomy","description":"Generates a SILVA fixed-rank taxonomy.","usage":"qiime rescript parse-silva-taxonomy [OPTIONS]","options":[{"names":["--i-taxonomy-map"],"argument":"ARTIFACT FeatureData[SILVATaxidMap]","description":"SILVA taxonomy map. This file contains a mapping of the sequence accessions to the numeric taxonomy identifiers and species label information. The SILVA release filename is typically in the form of: 'taxmap_slv_ssu_ref_X.txt', or 'taxmap_slv_ssu_ref_nr_X.txt' where 'X' is the SILVA version number. [required]"},{"names":["--i-taxonomy-ranks"],"argument":"ARTIFACT FeatureData[SILVATaxonomy]","description":"SILVA taxonomy file. This file contains the taxonomic rank information for each numeric taxonomy identifier and the taxonomy. The SILVA filename typically takes the form of: 'tax_slv_ssu_X.txt', where 'X' is the SILVA version number. [required]"},{"names":["--i-taxonomy-tree"],"argument":"ARTIFACT","description":"Phylogeny[Rooted] SILVA hierarchical taxonomy tree. The SILVA release"},{"names":["--p-rank-propagation","--p-no-rank-propagation"],"argument":"","description":"If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for 'f__Pasteurellaceae; g__'then the 'f__' rank will be propagated to become: 'f__Pasteurellaceae; g__Pasteurellaceae'."},{"names":["--p-include-species-labels","--p-no-include-species-labels"],"argument":"","description":"Include species rank labels in taxonomy output. Note: species-labels may not be reliable in all cases. [default: False]"},{"names":["--o-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"The resulting fixed-rank formatted SILVA taxonomy."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"reverse-transcribe","description":"Reverse transcribe RNA to DNA sequences.","usage":"qiime rescript reverse-transcribe [OPTIONS]","options":[{"names":["--i-rna-sequences"],"argument":"ARTIFACT FeatureData","description":"RNA Sequences to reverse transcribe to DNA. [required]"},{"names":["--o-dna-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]","description":"Reverse-transcribed DNA sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"subsample-fasta","description":"Subsample an indicated number of sequences from a FASTA file.","usage":"qiime rescript subsample-fasta [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]","description":"Sequences to subsample from. [required]"},{"names":["--o-sample-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]","description":"Sample of original sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"trim-alignment","description":"Trim alignment based on provided primers or specific positions.","usage":"qiime rescript trim-alignment [OPTIONS]","options":[{"names":["--i-aligned-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Aligned DNA sequences. [required]"},{"names":["--p-primer-fwd"],"argument":"TEXT","description":"Forward primer used to find the start position for alignment trimming. [optional]"},{"names":["--p-primer-rev"],"argument":"TEXT","description":"Reverse primer used to find the end position for alignment trimming. [optional]"},{"names":["--p-position-start"],"argument":"INTEGER","description":"Position within the alignment where the trimming will begin."},{"names":["--p-position-end"],"argument":"INTEGER","description":"Position within the alignment where the trimming will end."},{"names":["--o-trimmed-sequences"],"argument":"ARTIFACT FeatureData[AlignedSequence]","description":"Trimmed sequence alignment. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"sample-classifier","description":"Plugin for machine learning prediction of sample","usage":"qiime sample-classifier [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"classify-samples","description":"Train and test a cross-validated supervised","usage":"qiime sample-classifier classify-samples [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Categorical metadata column to use as prediction target. [required]"},{"names":["--p-test-size"],"argument":"PROPORTION","description":"Fraction of input samples to exclude from training set and use for classifier testing."},{"names":["--p-step"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"If optimize-feature-selection is True, step is the percentage of features to remove at each iteration."},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-estimator"],"argument":"{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}","description":"Estimator method to use for sample prediction."},{"names":["--p-optimize-feature-selection","--p-no-optimize-feature-selection"],"argument":"","description":"Automatically optimize input feature selection using recursive feature elimination."},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-palette"],"argument":"TEXT","description":"The color palette to use for plotting."},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Classifier]","description":"Trained sample estimator. [required]"},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy."},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[ClassifierPredictions]","description":"Predicted target values for each input sample."},{"names":["--o-model-summary"],"argument":"VISUALIZATION","description":"Summarized parameter and (if enabled) feature selection information for the trained estimator."},{"names":["--o-accuracy-results"],"argument":"VISUALIZATION","description":"Accuracy results visualization. [required]"},{"names":["--o-probabilities"],"argument":"ARTIFACT SampleData[Probabilities]","description":"Predicted class probabilities for each input sample. [required]"},{"names":["--o-heatmap"],"argument":"VISUALIZATION","description":"A heatmap of the top 50 most important features from the table. [required]"},{"names":["--o-training-targets"],"argument":"ARTIFACT SampleData[TrueTargets]","description":"Series containing true target values of train samples [required]"},{"names":["--o-test-targets"],"argument":"ARTIFACT SampleData[TrueTargets]","description":"Series containing true target values of test samples [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-samples-from-dist","description":"Run k-nearest-neighbors on a labeled distance","usage":"qiime sample-classifier classify-samples-from-dist [OPTIONS]","options":[{"names":["--i-distance-matrix"],"argument":"ARTIFACT","description":"DistanceMatrix a distance matrix [required]"},{"names":["--p-k"],"argument":"INTEGER","description":"Number of nearest neighbors [default: 1]"},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel."},{"names":["--p-palette"],"argument":"TEXT","description":"The color palette to use for plotting."},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Categorical metadata column to use as prediction target. [required]"},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[ClassifierPredictions]","description":"leave one out predictions for each sample [required]"},{"names":["--o-accuracy-results"],"argument":"VISUALIZATION","description":"Accuracy results visualization. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"classify-samples-ncv","description":"Nested cross-validated supervised learning","usage":"qiime sample-classifier classify-samples-ncv [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Categorical metadata column to use as prediction target. [required]"},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-estimator"],"argument":"{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}","description":"Estimator method to use for sample prediction."},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-predictions"],"argument":"ARTIFACT SampleData[ClassifierPredictions]","description":"Predicted target values for each input sample."},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy."},{"names":["--o-probabilities"],"argument":"ARTIFACT SampleData[Probabilities]","description":"Predicted class probabilities for each input sample."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"confusion-matrix","description":"Make a confusion matrix from sample classifier","usage":"qiime sample-classifier confusion-matrix [OPTIONS]","options":[{"names":["--i-predictions"],"argument":"ARTIFACT SampleData[ClassifierPredictions]","description":"Predicted values to plot on x axis. Should be predictions of categorical data produced by a sample classifier. [required]"},{"names":["--i-probabilities"],"argument":"ARTIFACT SampleData[Probabilities]","description":"Predicted class probabilities for each input sample."},{"names":["--m-truth-file","--m-truth-column"],"argument":"METADATA","description":"Metadata column (true values) to plot on y axis."},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fit-classifier","description":"Fit a supervised learning classifier.","usage":"qiime sample-classifier fit-classifier [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Numeric metadata column to use as prediction target."},{"names":["--p-step"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"If optimize-feature-selection is True, step is the percentage of features to remove at each iteration. [required]"},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-estimator"],"argument":"{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}","description":"Estimator method to use for sample prediction."},{"names":["--p-optimize-feature-selection","--p-no-optimize-feature-selection"],"argument":"","description":"Automatically optimize input feature selection using recursive feature elimination. [default: False]"},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. [default: False]"},{"names":["--p-missing-samples"],"argument":"TEXT Choices('error', 'ignore')","description":"How to handle missing samples in metadata. \"error\" will fail if missing samples are detected. \"ignore\" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: 'error']"},{"names":["--o-sample-estimator"],"argument":"ARTIFACT SampleEstimator[Classifier]","description":"Trained sample classifier. [required]"},{"names":["--o-feature-importance"],"argument":"ARTIFACT FeatureData[Importance]","description":"Importance of each input feature to model accuracy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fit-regressor","description":"Fit a supervised learning regressor.","usage":"qiime sample-classifier fit-regressor [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT","description":"Feature table containing all features that should be used for target prediction. [required]"},{"names":["--m-metadata-file","--m-metadata-column"],"argument":"METADATA","description":"Numeric metadata column to use as prediction target. [required]"},{"names":["--p-step"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_start=False)","description":"If optimize-feature-selection is True, step is the percentage of features to remove at each iteration."},{"names":["--p-cv"],"argument":"INTEGER","description":"Number of k-fold cross-validations to perform."},{"names":["--p-random-state"],"argument":"INTEGER","description":"Seed used by random number generator. [optional]"},{"names":["--p-n-jobs"],"argument":"NTHREADS","description":"Number of jobs to run in parallel. [default: 1]"},{"names":["--p-n-estimators"],"argument":"INTEGER","description":"Number of trees to grow for estimation."},{"names":["--p-estimator"],"argument":"{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor[DecisionTree], AdaBoostRegressor[ExtraTrees], ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}","description":"Estimator method to use for sample prediction."},{"names":["--p-optimize-feature-selection","--p-no-optimize-feature-selection"],"argument":"","description":"Automatically optimize input feature selection using recursive feature elimination. [default: False]"},{"names":["--p-parameter-tuning","--p-no-parameter-tuning"],"argument":"","description":"Automatically tune hyperparameters using random grid search. 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[required]"},{"names":["--o-hits"],"argument":"ARTIFACT","description":"Output files produced by Kraken2. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. 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Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"collate-kraken2-outputs","description":"Collate kraken2 outputs","usage":"qiime moshpit collate-kraken2-outputs [OPTIONS]","options":[{"names":["--i-kraken2-outputs"],"argument":"ARTIFACTS...","description":"[required]"},{"names":["--o-collated-kraken2-outputs"],"argument":"ARTIFACTS...","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"collate-kraken2-reports","description":"Collate kraken2 reports","usage":"qiime moshpit collate-kraken2-reports [OPTIONS]","options":[{"names":["--i-kraken2-reports"],"argument":"ARTIFACTS...","description":"[required]"},{"names":["--o-collated-kraken2-reports"],"argument":"ARTIFACTS...","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. 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[required]"},{"names":["--o-feature-table"],"argument":"ARTIFACT","description":"Mapping between MAGs and samples. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"eggnog-annotate","description":"Annotate orthologs against eggNOG database","usage":"qiime moshpit eggnog-annotate [OPTIONS]","options":[{"names":["--i-eggnog-hits"],"argument":"ARTIFACT","description":"SampleData[BLAST6] BLAST6-like table(s) describing the identified orthologs. 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QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"estimate-bracken","description":"Perform read abundance re-estimation using Bracken.","usage":"qiime moshpit estimate-bracken [OPTIONS]","options":[{"names":["--i-kraken-reports"],"argument":"ARTIFACT SampleData","description":"Reports produced by Kraken2. [required]"},{"names":["--i-bracken-db"],"argument":"ARTIFACT","description":"BrackenDB Bracken database. 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[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"evaluate-busco","description":"Evaluate quality of the generated MAGs using BUSCO.","usage":"qiime moshpit evaluate-busco [OPTIONS]","options":[{"names":["--i-bins"],"argument":"ARTIFACT","description":"MAGs to be analyzed. 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IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fetch-diamond-db","description":"Fetch the complete Diamond database necessary to run the eggnog-diamond-search action.","usage":"qiime moshpit fetch-diamond-db [OPTIONS]","options":[{"names":["--o-diamond-db"],"argument":"ARTIFACT","description":"Complete Diamond reference database. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fetch-eggnog-db","description":"Fetch the databases necessary to run the eggnog-annotate action.","usage":"qiime moshpit fetch-eggnog-db [OPTIONS]","options":[{"names":["--o-eggnog-db"],"argument":"ARTIFACT","description":"Artifact containing the eggNOG annotation database. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fetch-eggnog-proteins","description":"Fetch the databases necessary to run the build-eggnog-diamond-db action.","usage":"qiime moshpit fetch-eggnog-proteins [OPTIONS]","options":[{"names":["--o-eggnog-proteins"],"argument":"ARTIFACT","description":"eggNOG database of protein sequences and their corresponding taxonomy information. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fetch-kaiju-db","description":"Fetch Kaiju database.","usage":"qiime moshpit fetch-kaiju-db [OPTIONS]","options":[{"names":["--p-database-type"],"argument":"{nr, nr_euk, refseq, fungi, viruses, plasmids, progenomes, rvdb}","description":"Type of database to be downloaded. [required]"},{"names":["--o-database"],"argument":"ARTIFACT","description":"Kaiju database. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fetch-ncbi-taxonomy","description":"Fetch NCBI reference taxonomy","usage":"qiime moshpit fetch-ncbi-taxonomy [OPTIONS]","options":[{"names":["--o-taxonomy"],"argument":"ARTIFACT","description":"NCBI reference taxonomy. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-derep-mags","description":"Filter dereplicated MAGs.","usage":"qiime moshpit filter-derep-mags [OPTIONS]","options":[{"names":["--i-mags"],"argument":"ARTIFACT","description":"Dereplicated MAGs to filter. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata indicating which MAG ids to filter. [required]"},{"names":["--p-where"],"argument":"TEXT","description":"Optional SQLite WHERE clause specifying MAG metadata criteria that must be met to be included in the filtered data. If not provided, all MAGs in `metadata` that are also in the MAG data will be retained."},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"Defaults to False. If True, the MAGs selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]"},{"names":["--o-filtered-mags"],"argument":"ARTIFACT","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-mags","description":"Filter MAGs.","usage":"qiime moshpit filter-mags [OPTIONS]","options":[{"names":["--i-mags"],"argument":"ARTIFACT","description":"MAGs to filter. [required]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"Sample metadata indicating which MAG ids to filter. [required]"},{"names":["--p-where"],"argument":"TEXT","description":"Optional SQLite WHERE clause specifying MAG metadata criteria that must be met to be included in the filtered data. If not provided, all MAGs in `metadata` that are also in the MAG data will be retained."},{"names":["--p-exclude-ids","--p-no-exclude-ids"],"argument":"","description":"Defaults to False. If True, the MAGs selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]"},{"names":["--p-on"],"argument":"TEXT Choices('sample', 'mag')","description":"Whether to filter based on sample or MAG metadata."},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"(multiple Sample metadata indicating which MAG ids to filter."},{"names":["--o-filtered-mags"],"argument":"ARTIFACT","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"get-feature-lengths","description":"Get feature lengths.","usage":"qiime moshpit get-feature-lengths [OPTIONS]","options":[{"names":["--i-features"],"argument":"ARTIFACT","description":"Features to get lengths for. [required]"},{"names":["--o-lengths"],"argument":"ARTIFACT","description":"Feature lengths. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"inspect-kraken2-db","description":"Inspect a Kraken 2 database.","usage":"qiime moshpit inspect-kraken2-db [OPTIONS]","options":[{"names":["--i-db"],"argument":"ARTIFACT","description":"The Kraken 2 database for which to generate the report. [required]"},{"names":["--p-threads"],"argument":"INTEGER","description":"The number of threads to use.   Range(1, None) [default: 1]"},{"names":["--o-report"],"argument":"ARTIFACT","description":"The report of the supplied database. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"kraken2-to-features","description":"Select downstream features from Kraken 2","usage":"qiime moshpit kraken2-to-features [OPTIONS]","options":[{"names":["--i-reports"],"argument":"ARTIFACT","description":"Per-sample Kraken 2 reports. [required]"},{"names":["--p-coverage-threshold"],"argument":"NUMBER","description":"The minimum percent coverage required to produce a feature. [default: 0.1]"},{"names":["--o-table"],"argument":"ARTIFACT","description":"A presence/absence table of selected features. The features are not of even ranks, but will be the most specific rank available. [required]"},{"names":["--o-taxonomy"],"argument":"ARTIFACT","description":"Infra-clade ranks are ignored unless they are strain-level. Missing internal ranks are annotated by their next most specific rank, with the exception of k__Bacteria and k__Archaea which match their domain's name. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"kraken2-to-mag-features","description":"Select downstream MAG features from Kraken 2","usage":"qiime moshpit kraken2-to-mag-features [OPTIONS]","options":[{"names":["--i-reports"],"argument":"ARTIFACT","description":"Per-sample Kraken 2 reports. [required]"},{"names":["--i-hits"],"argument":"ARTIFACT","description":"Per-sample Kraken 2 output files. [required]"},{"names":["--p-coverage-threshold"],"argument":"NUMBER","description":"The minimum percent coverage required to produce a feature. [default: 0.1]"},{"names":["--o-taxonomy"],"argument":"ARTIFACT","description":"Infra-clade ranks are ignored unless they are strain-level. Missing internal ranks are annotated by their next most specific rank, with the exception of k__Bacteria and k__Archaea which match their domain's name. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partition-feature-data-mags","description":"Partition MAGs","usage":"qiime moshpit partition-feature-data-mags [OPTIONS]","options":[{"names":["--i-mags"],"argument":"ARTIFACT","description":"MAGs to partition. [required]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the MAGs into."},{"names":["--o-partitioned-mags"],"argument":"ARTIFACTS...","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partition-orthologs","description":"Partition orthologs","usage":"qiime moshpit partition-orthologs [OPTIONS]","options":[{"names":["--i-orthologs"],"argument":"ARTIFACT","description":"The orthologs to partition. [required]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"The number of partitions to split the MAGs into."},{"names":["--o-partitioned-orthologs"],"argument":"ARTIFACTS...","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"partition-sample-data-mags","description":"Partition MAGs","usage":"qiime moshpit partition-sample-data-mags [OPTIONS]","options":[{"names":["--i-mags"],"argument":"ARTIFACT","description":"The MAGs to partition. [required]"},{"names":["--p-num-partitions"],"argument":"INTEGER","description":"Range(1, None) The number of partitions to split the MAGs into."},{"names":["--o-partitioned-mags"],"argument":"ARTIFACTS...","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"predict-genes-prodigal","description":"Predict gene sequences from MAGs using Prodigal.","usage":"qiime moshpit predict-genes-prodigal [OPTIONS]","options":[{"names":["--i-mags"],"argument":"ARTIFACT","description":"MAGs for which one wishes to predict genes. [required]"},{"names":["--p-translation-table-number"],"argument":"TEXT","description":"Translation table to be used to translate genes into a sequence of amino acids.."},{"names":["--o-loci"],"argument":"ARTIFACT","description":"Gene coordinates files (one per MAG) listing the location of each predicted gene as well as some additional scoring information. [required]"},{"names":["--o-genes"],"argument":"ARTIFACT","description":"Fasta files (one per MAG) with the nucleotide sequences of the predicted genes. [required]"},{"names":["--o-proteins"],"argument":"ARTIFACT GenomeData[Proteins]","description":"Fasta files (one per MAG) with the protein translation of the predicted genes. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"taxa","description":"Plugin for working with feature taxonomy annotations.","usage":"qiime taxa [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"barplot","description":"Visualize taxonomy with an interactive bar plot","usage":"qiime taxa barplot [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency | PresenceAbsence]","description":"Feature table to visualize at various taxonomic levels. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. If no taxonomy is provided, the feature IDs will be used as labels. [optional]"},{"names":["--m-metadata-file"],"argument":"METADATA...","description":"The sample metadata."},{"names":["--p-level-delimiter"],"argument":"TEXT","description":"Attempt to parse hierarchical taxonomic information from feature IDs by separating levels with this character. This parameter is ignored if a taxonomy is provided as input. [optional]"},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"collapse","description":"Collapse features by their taxonomy at the specified level","usage":"qiime taxa collapse [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table to be collapsed. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]"},{"names":["--p-level"],"argument":"INTEGER","description":"The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]"},{"names":["--o-collapsed-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-seqs","description":"Taxonomy-based feature sequence filter.","usage":"qiime taxa filter-seqs [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Feature sequences to be filtered. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic annotations for features in the provided feature sequences. All features in the feature sequences must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature sequences will be ignored. [required]"},{"names":["--p-include"],"argument":"TEXT","description":"One or more search terms that indicate which taxa should be included in the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional]"},{"names":["--p-exclude"],"argument":"TEXT","description":"One or more search terms that indicate which taxa should be excluded from the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional]"},{"names":["--p-query-delimiter"],"argument":"TEXT","description":"The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ',']"},{"names":["--p-mode"],"argument":"TEXT Choices('exact', 'contains')","description":"Mode for determining if a search term matches a taxonomic annotation. \"contains\" requires that the annotation has the term as a substring; \"exact\" requires that the annotation is a perfect match to a search term. [default: 'contains']"},{"names":["--o-filtered-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The taxonomy-filtered feature sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"filter-table","description":"Taxonomy-based feature table filter.","usage":"qiime taxa filter-table [OPTIONS]","options":[{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency¹ | PresenceAbsence²]","description":"Feature table to be filtered. [required]"},{"names":["--i-taxonomy"],"argument":"ARTIFACT FeatureData[Taxonomy]","description":"Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored. [required]"},{"names":["--p-include"],"argument":"TEXT","description":"One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional]"},{"names":["--p-exclude"],"argument":"TEXT","description":"One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional]"},{"names":["--p-query-delimiter"],"argument":"TEXT","description":"The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations."},{"names":["--p-mode"],"argument":"TEXT Choices('exact', 'contains')","description":"Mode for determining if a search term matches a taxonomic annotation. \"contains\" requires that the annotation has the term as a substring; \"exact\" requires that the annotation is a perfect match to a search term. [default: 'contains']"},{"names":["--o-filtered-table"],"argument":"ARTIFACT FeatureTable[Frequency¹ | PresenceAbsence²]","description":"The taxonomy-filtered feature table. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]},{"name":"vsearch","description":"Plugin for clustering and dereplicating with vsearch.","usage":"qiime vsearch [OPTIONS] COMMAND [ARGS]...","options":[{"names":["--version"],"argument":"","description":"Show the version and exit."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}],"subcommands":[{"name":"cluster-features-closed-reference","description":"Closed-reference clustering of features.","usage":"qiime vsearch cluster-features-closed-reference [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT","description":"The sequences corresponding to the features in table. [required]"},{"names":["--i-table"],"argument":"ARTIFACT","description":"The feature table to be clustered. [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences to use as cluster centroids. [required]"},{"names":["--p-perc-identity"],"argument":"","description":"The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required]"},{"names":["--p-strand"],"argument":"{'plus', 'both'}","description":"Search plus (i.e., forward) or both (i.e., forward and reverse complement) strands. [default: 'plus']"},{"names":["--p-threads"],"argument":"INTEGER","description":"The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1]"},{"names":["--o-clustered-table"],"argument":"ARTIFACT","description":"The table following clustering of features. [required]"},{"names":["--o-clustered-sequences"],"argument":"ARTIFACT","description":"The sequences representing clustered features, relabeled by the reference IDs. [required]"},{"names":["--o-unmatched-sequences"],"argument":"ARTIFACT","description":"The sequences which failed to match any reference sequences. This output maps to vsearch's --notmatched parameter. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cluster-features-de-novo","description":"De novo clustering of features.","usage":"qiime vsearch cluster-features-de-novo [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The sequences corresponding to the features in table. [required]"},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The feature table to be clustered. [required]"},{"names":["--p-strand"],"argument":"TEXT Choices('plus', 'both')","description":"Search plus (i.e., forward) or both (i.e., forward and reverse complement) strands. [default: 'plus']"},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of threads to use for computation. Passing 0 will launch one thread per CPU core."},{"names":["--o-clustered-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The table following clustering of features."},{"names":["--o-clustered-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"Sequences representing clustered features."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"cluster-features-open-reference","description":"Open-reference clustering of features.","usage":"qiime vsearch cluster-features-open-reference [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT","description":"The sequences corresponding to the features in table. [required]"},{"names":["--i-table"],"argument":"ARTIFACT","description":"The feature table to be clustered. [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT","description":"The sequences to use as cluster centroids. [required]"},{"names":["--p-perc-identity"],"argument":"PROPORTION","description":"The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required]"},{"names":["--p-strand"],"argument":"{'plus', 'both'}","description":"Search plus (i.e., forward) or both (i.e., forward and reverse complement) strands. [default: 'plus']"},{"names":["--p-threads"],"argument":"INTEGER","description":"The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1]"},{"names":["--o-clustered-table"],"argument":"ARTIFACT","description":"The table following clustering of features. [required]"},{"names":["--o-clustered-sequences"],"argument":"ARTIFACT","description":"Sequences representing clustered features. [required]"},{"names":["--o-new-reference-sequences"],"argument":"ARTIFACT","description":"The new reference sequences. This can be used for subsequent runs of open-reference clustering for consistent definitions of features across open-reference feature tables. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--recycle-pool"],"argument":"TEXT","description":"Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using."},{"names":["--no-recycle"],"argument":"","description":"Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling."},{"names":["--parallel"],"argument":"","description":"Execute your action in parallel. This flag will use your default parallel config."},{"names":["--parallel-config"],"argument":"FILE","description":"Execute your action in parallel using a config at the indicated path."},{"names":["--use-cache"],"argument":"DIRECTORY","description":"Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"dereplicate-sequences","description":"Dereplicate sequences.","usage":"qiime vsearch dereplicate-sequences [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT SampleData","description":"|   SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]"},{"names":["--i-sequences"],"argument":"ARTIFACT SampleDataSequences","description":"|   SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]"},{"names":["--p-derep-prefix","--p-no-derep-prefix"],"argument":"","description":"Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False]"},{"names":["--p-min-seq-length"],"argument":"INTEGER","description":"Discard sequences shorter than this integer."},{"names":["--p-min-unique-size"],"argument":"INTEGER","description":"Discard sequences with a post-dereplication"},{"names":["--o-dereplicated-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"The table of dereplicated sequences. [required]"},{"names":["--o-dereplicated-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The dereplicated sequences. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"fastq-stats","description":"Fastq stats with vsearch.","usage":"qiime vsearch fastq-stats [OPTIONS]","options":[{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of threads used for computation."},{"names":["--o-visualization"],"argument":"VISUALIZATION","description":"[required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"merge-pairs","description":"Merge paired-end reads.","usage":"qiime vsearch merge-pairs [OPTIONS]","options":[{"names":["--i-demultiplexed-seqs"],"argument":"","description":"ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be merged."},{"names":["--p-truncqual"],"argument":"INTEGER","description":"Truncate sequences at the first base with the specified quality score value or lower."},{"names":["--p-minlen"],"argument":"INTEGER","description":"Sequences shorter than minlen after truncation are discarded."},{"names":["--p-maxns"],"argument":"INTEGER","description":"Sequences with more than maxns N characters are discarded."},{"names":["--p-allowmergestagger","--p-no-allowmergestagger"],"argument":"","description":"Allow merging of staggered read pairs."},{"names":["--p-minovlen"],"argument":"INTEGER","description":"Minimum length of the area of overlap between reads during merging."},{"names":["--p-maxdiffs"],"argument":"INTEGER","description":"Maximum number of mismatches in the area of overlap during merging."},{"names":["--p-minmergelen"],"argument":"INTEGER","description":"Minimum length of the merged read to be retained."},{"names":["--p-maxmergelen"],"argument":"INTEGER","description":"Maximum length of the merged read to be retained."},{"names":["--p-maxee"],"argument":"NUMBER","description":"Maximum number of expected errors in the merged read to be retained."},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of threads to use for computation."},{"names":["--o-merged-sequences"],"argument":"ARTIFACT SampleData[JoinedSequencesWithQuality]","description":"The merged sequences. [required]"},{"names":["--o-unmerged-sequences"],"argument":"ARTIFACT","description":"The unmerged paired-end reads. [required]"},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"uchime-denovo","description":"De novo chimera filtering with vsearch.","usage":"qiime vsearch uchime-denovo [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The feature sequences to be chimera-checked."},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table (used for computing total feature abundances). [required]"},{"names":["--p-dn"],"argument":"NUMBER","description":"No vote pseudo-count, corresponding to the"},{"names":["--p-mindiffs"],"argument":"INTEGER","description":"Minimum number of differences per segment."},{"names":["--p-mindiv"],"argument":"NUMBER","description":"Minimum divergence from closest parent."},{"names":["--p-minh"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]"},{"names":["--p-xn"],"argument":"NUMBER Range(1.0, None, inclusive_start=False)","description":"No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]"},{"names":["--o-chimeras"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The chimeric sequences. [required]"},{"names":["--o-nonchimeras"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The non-chimeric sequences. [required]"},{"names":["--o-stats"],"argument":"ARTIFACT","description":"Summary statistics from chimera checking."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]},{"name":"uchime-ref","description":"Reference-based chimera filtering with","usage":"qiime vsearch uchime-ref [OPTIONS]","options":[{"names":["--i-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The feature sequences to be chimera-checked."},{"names":["--i-table"],"argument":"ARTIFACT FeatureTable[Frequency]","description":"Feature table (used for computing total feature abundances). [required]"},{"names":["--i-reference-sequences"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The non-chimeric reference sequences. [required]"},{"names":["--p-dn"],"argument":"NUMBER","description":"No vote pseudo-count, corresponding to the"},{"names":["--p-mindiffs"],"argument":"INTEGER","description":"Minimum number of differences per segment."},{"names":["--p-mindiv"],"argument":"NUMBER","description":"Minimum divergence from closest parent."},{"names":["--p-minh"],"argument":"PROPORTION Range(0.0, 1.0, inclusive_end=True)","description":"Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]"},{"names":["--p-xn"],"argument":"NUMBER Range(1.0, None, inclusive_start=False)","description":"No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]"},{"names":["--p-threads"],"argument":"NTHREADS","description":"The number of threads to use for computation. Passing 0 will launch one thread per CPU core."},{"names":["--o-chimeras"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The chimeric sequences. [required]"},{"names":["--o-nonchimeras"],"argument":"ARTIFACT FeatureData[Sequence]","description":"The non-chimeric sequences. [required]"},{"names":["--o-stats"],"argument":"ARTIFACT","description":"Summary statistics from chimera checking."},{"names":["--output-dir"],"argument":"PATH","description":"Output unspecified results to a directory"},{"names":["--verbose","--quiet"],"argument":"","description":"Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden)."},{"names":["--example-data"],"argument":"PATH","description":"Write example data and exit."},{"names":["--citations"],"argument":"","description":"Show citations and exit."},{"names":["--help"],"argument":"","description":"Show this message and exit."}]}]}],"version":"q2cli version 2024.5.0"}
diff --git a/bio/yaml/qiime.yaml b/bio/yaml/qiime.yaml
index 15d968bd..8250db1d 100644
--- a/bio/yaml/qiime.yaml
+++ b/bio/yaml/qiime.yaml
@@ -721,9 +721,9 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: composition
-    description: Plugin for compositional data analysis.
-    usage: qiime composition [OPTIONS] COMMAND [ARGS]...
+  - name: assembly
+    description: QIIME 2 plugin for (meta)genome assembly.
+    usage: qiime assembly [OPTIONS] COMMAND [ARGS]...
     options:
       - names:
           - --version
@@ -737,78 +737,123 @@ subcommands:
           - --citations
         argument: ""
         description: Show citations and exit.
+      - names:
+          - --show-hidden-actions
+        argument: ""
+        description: This plugin has hidden actions with names starting with '_'. These are generally called internally by pipelines. Passing this flag will display those actions.
       - names:
           - --help
         argument: ""
         description: Show this message and exit.
     subcommands:
-      - name: add-pseudocount
-        description: Add pseudocount to table.
-        usage: qiime composition add-pseudocount [OPTIONS]
+      - name: assemble-megahit
+        description: Assemble contigs using MEGAHIT.
+        usage: qiime assembly assemble-megahit [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table to which pseudocounts should be added. [required]
+            - --i-seqs
+            argument: ARTIFACT
+            description: The paired- or single-end sequences to be assembled. [required]
           - names:
-              - --p-pseudocount
+            - --p-presets
+            argument: '{meta, meta-sensitive, meta-large, disabled}'
+            description: Override a group of parameters. See the megahit documentation for details.
+          - names:
+              - --p-min-count
             argument: INTEGER
-            description: The value to add to all counts in the feature table.
+            description: Minimum multiplicity for filtering (k_min+1)-mers.
           - names:
-              - --o-composition-table
-            argument: ARTIFACT FeatureTable[Composition]
-            description: The resulting feature table. [required]
+              - --p-k-list
+            argument: INTEGERS...
+            description: List of kmer size - all must be odd with an increment <= 28.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-k-min
+            argument: INTEGER
+            description: Minimum kmer size (<= 255), must be odd number. Overrides k-list. [optional]
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --p-k-max
+            argument: INTEGER
+            description: Maximum kmer size (<= 255), must be odd number. Overrides k-list. [optional]
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-k-step
+            argument: INTEGER
+            description: Increment of kmer size of each iteration (<= 28), must be even number. Overrides k-list. [optional]
           - names:
-              - --citations
+              - --p-no-mercy
+              - --p-no-no-mercy
             argument: ""
-            description: Show citations and exit.
+            description: 'Do not add mercy kmers. [default: False]'
           - names:
-              - --help
+              - --p-bubble-level
+            argument: INTEGER
+            description: Intensity of bubble merging, 0 to disable.
+          - names:
+              - --p-prune-level
+            argument: INTEGER
+            description: 'Strength of low depth pruning. [default: 2]'
+          - names:
+              - --p-prune-depth
+            argument: INTEGER
+            description: Remove unitigs with avg kmer depth less than this value.
+          - names:
+              - --p-disconnect-ratio
+            argument: PROPORTION
+            description: 'Disconnect unitigs if its depth is less than this ratio times the total depth of itself and its siblings. [default: 0.1]'
+          - names:
+              - --p-low-local-ratio
+            argument: PROPORTION
+            description: Remove unitigs if its depth is less than this ratio times the average depth of the neighborhoods.
+          - names:
+              - --p-max-tip-len
+            argument: VALUE
+            description: Remove tips less than this value.
+          - names:
+              - --p-cleaning-rounds
+            argument: INTEGER
+            description: 'Number of rounds for graph cleanning. [default: 5]'
+          - names:
+              - --p-no-local
+              - --p-no-no-local
             argument: ""
-            description: Show this message and exit.
-      - name: ancom
-        description: Apply ANCOM to identify features that differ in abundance.
-        usage: qiime composition ancom [OPTIONS]
-        options:
+            description: 'Disable local assembly. [default: False]'
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Composition]
-            description: The feature table to be used for ANCOM computation.
+              - --p-kmin-1pass
+              - --p-no-kmin-1pass
+            argument: ""
+            description: Use 1pass mode to build SdBG of k-min.
           - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: The categorical sample metadata column to test for differential abundance across. [required]
+              - --p-memory
+            argument: NUMBER
+            description: Max memory in byte to be used in SdBG construction
           - names:
-              - --p-transform-function
-            argument: TEXT Choices('sqrt', 'log', 'clr')
-            description: 'The method applied to transform feature values before generating volcano plots. [default: ''clr'']'
+              - --p-mem-flag
+            argument: INTEGER
+            description: "SdBG builder memory mode. 0: minimum; 1: moderate; others: use all memory specified by '-m/--memory'."
           - names:
-              - --p-difference-function
-            argument: TEXT Choices('mean_difference', 'f_statistic')
-            description: The method applied to visualize fold difference in feature abundances across groups for volcano plots.
+              - --p-num-cpu-threads
+            argument: INTEGER
+            description: 'Number of CPU threads. [default: 1]'
           - names:
-              - --p-filter-missing
-              - --p-no-filter-missing
+              - --p-no-hw-accel
+              - --p-no-no-hw-accel
             argument: ""
-            description: 'If True, samples with missing metadata values will be filtered from the table prior to analysis. If False, an error will be raised if there are any missing metadata values. [default: False]'
+            description: 'Run MEGAHIT without BMI2 and POPCNT hardware instructions. [default: False]'
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --p-min-contig-len
+            argument: INTEGER
+            description: 'Minimum length of contigs to output. [default: 200]'
+          - names:
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the contigs into.
+          - names:
+              - --p-coassemble
+            argument: VALUE
+            description:  Co-assemble reads into contigs from all samples.
+          - names:
+              - --o-contigs
+            argument: ARTIFACT
+            description: The resulting assembled contigs. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -818,6 +863,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -830,60 +895,102 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: ancombc
-        description: Analysis of Composition of Microbiomes with Bias Correction
-        usage: qiime composition ancombc [OPTIONS]
+      - name: assemble-spades
+        description: Assemble contigs using SPAdes.
+        usage: qiime assembly assemble-spades [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table to be used for ANCOM-BC computation. [required]
+            - --i-seqs
+            argument: ARTIFACT
+            description: The paired- or single-end sequences to be assembled. [required]
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata.
+              - --p-isolate
+              - --p-no-isolate
+            argument: ""
+            description: 'This flag is highly recommended for high-coverage isolate and multi-cell data. [default: False]'
           - names:
-              - --p-formula
-            argument: TEXT
-            description: How the microbial absolute abundances for each taxon depend on the variables within the `metadata`.
+              - --p-sc
+              - --p-no-sc
+            argument: ""
+            description: This flag is required for MDA (single-cell) data.
           - names:
-              - --p-p-adj-method
-            argument: TEXT
-            description: "Method to adjust p-values. Choices('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')"
+              - --p-meta
+              - --p-no-meta
+            argument: ""
+            description: 'This flag is required for metagenomic data. This option is only supported in combination with paired-end reads. [default: False]'
           - names:
-              - --p-prv-cut
-            argument: NUMBER
-            description: 'A numerical fraction between 0-1. Taxa with prevalences less than this value will be excluded from the analysis. [default: 0.1]'
+              - --p-bio
+              - --p-no-bio
+            argument: ""
+            description: This flag is required for biosyntheticSPAdes mode.
           - names:
-              - --p-lib-cut
-            argument: INTEGER
-            description: A numerical threshold for filtering samples based on library sizes. Samples with library sizes less than this value will be excluded from the analysis.
-
+              - --p-corona
+              - --p-no-corona
+            argument: ""
+            description: This flag is required for coronaSPAdes mode.
           - names:
-              - --p-reference-levels
-            argument: TEXT...
-            description: Define the reference level(s) to be used for categorical columns found in the `formula`.
+              - --p-plasmid
+              - --p-no-plasmid
+            argument: ""
+            description: Runs plasmidSPAdes pipeline for plasmid detection.
           - names:
-              - --p-tol
-            argument: NUMBER
-            description: 'The iteration convergence tolerance for the E-M algorithm. [default: 1e-05]'
+              - --p-metaviral
+              - --p-no-metaviral
+            argument: ""
+            description: Runs metaviralSPAdes pipeline for virus detection.
           - names:
-              - --p-max-iter
+              - --p-metaplasmid
+              - --p-no-metaplasmid
+            argument: ""
+            description: 'Runs metaplasmidSPAdes pipeline for plasmid detection in metagenomic datasets (equivalent for --meta --plasmid). [default: False]'
+          - names:
+              - --p-only-assembler
+              - --p-no-only-assembler
+            argument: ""
+            description: 'Runs only assembling (without read error correction). [default: False]'
+          - names:
+              - --p-careful
+              - --p-no-careful
+            argument: ""
+            description: 'Tries to reduce number of mismatches and short indels. [default: False]'
+          - names:
+              - --p-disable-rr
+              - --p-no-disable-rr
+            argument: ""
+            description: Disables repeat resolution stage of assembling.
+          - names:
+              - --p-threads
             argument: INTEGER
-            description: 'The maximum number of iterations for the E-M algorithm. [default: 100]'
+            description: Number of threads.
           - names:
-              - --p-conserve
-              - --p-no-conserve
+              - --p-memory
+            argument: INTEGER
+            description: RAM limit for SPAdes in Gb.
+          - names:
+              - --p-k
+            argument: VALUES...
+            description: 'List of k-mer sizes (must be odd and less than 128). [default: [''auto'']]'
+          - names:
+              - --p-cov-cutoff
+            argument: VALUES...
+            description: Coverage cutoff value (a positive float number, or 'auto', or 'off').
+          - names:
+              - --p-phred-offset
+            argument: TEXT Choices('auto-detect', '33', '64')
+            description: PHRED quality offset in the input reads (33 or 64).
+          - names:
+              - --p-debug
+              - --p-no-debug
             argument: ""
-            description: Whether to use a conservative variance estimator for the test statistic. It is recommended if the sample size is small and/or the number of differentially abundant taxa is believed to be large.
+            description: 'Runs SPAdes in debug mode. [default: False]'
           - names:
-              - --p-alpha
-            argument: NUMBER
-            description: 'Level of significance. [default: 0.05]'
+              - --p-coassemble
+            argument: VALUE
+            description:  Co-assemble reads into contigs from all samples.
           - names:
-              - --o-differentials
-            argument: ARTIFACT FeatureData[DifferentialAbundance]
-            description: The calculated per-feature differentials. [required]
+              - --o-contigs
+            argument: ARTIFACT
+            description: The resulting assembled contigs. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -905,53 +1012,50 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: da-barplot
-        description: Differential abundance bar plots
-        usage: qiime composition da-barplot [OPTIONS]
+      - name: collate-alignments
+        description: Map reads to contigs helper.
+        usage: qiime assembly collate-alignments [OPTIONS]
         options:
           - names:
-              - --i-data
-            argument: ARTIFACT FeatureData[DifferentialAbundance]
-            description: The ANCOM-BC output to be plotted. [required]
-          - names:
-              - --p-effect-size-label
-            argument: TEXT
-            description: 'Label for effect sizes in `data`. [default: ''lfc'']'
-          - names:
-              - --p-feature-id-label
-            argument: TEXT
-            description: 'Label for feature ids in `data`. [default: ''id'']'
+              - --i-alignments
+            argument: ARTIFACTS...
+            description: A collection of alignments to be collated. [required]
           - names:
-              - --p-error-label
-            argument: TEXT
-            description: Label for effect size errors in `data`.
+              - --o-collated-alignments
+            argument: ARTIFACT
+            description: The alignemnts collated into oine artifact [required]
           - names:
-              - --p-significance-label
-            argument: TEXT
-            description: Label for statistical significance level in `data`.
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-significance-threshold
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: Exclude features with statistical significance level greater (i.e., less significant) than this threshold.
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-level-delimiter
-            argument: TEXT
-            description: If feature ids encode hierarchical information, split the levels when generating feature labels in the visualization using this delimiter. [optional]
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-label-limit
-            argument: INTEGER
-            description: Set the maximum length that will be viewable for axis labels. You can set this parameter if your axis labels are being cut off. [optional]
+              - --citations
+            argument: ""
+            description: Show citations and exit.
           - names:
-              - --p-effect-size-threshold
-            argument: NUMBER
-            description: Exclude features with an absolute value of effect size less than this threshold.
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: collate-contigs
+        description: Collate contigs
+        usage: qiime assembly collate-contigs [OPTIONS]
+        options:
           - names:
-              - --m-feature-ids-file
-            argument: METADATA...
-            description: Exclude features if their ids are not included in this index.
+              - --i-contigs
+            argument: ARTIFACTS...
+            description: A collection of contigs to be collated. [required]
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
+              - --o-collated-contigs
+            argument: ARTIFACT
             description: '[required]'
           - names:
               - --output-dir
@@ -974,17 +1078,17 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: tabulate
-        description: View tabular output from ANCOM-BC.
-        usage: qiime composition tabulate [OPTIONS]
+      - name: collate-indices
+        description: Collate indices
+        usage: qiime assembly collate-indices [OPTIONS]
         options:
           - names:
-              - --i-data
-            argument: ARTIFACT FeatureData[DifferentialAbundance]
-            description: The ANCOM-BC output to be tabulated. [required]
+              - --i-indices
+            argument: ARTIFACTS...
+            description: A collection of indices to be collated. [required]
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
+              - --o-collated-indices
+            argument: ARTIFACT
             description: '[required]'
           - names:
               - --output-dir
@@ -1007,98 +1111,77 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: cutadapt
-    description: Plugin for removing adapter sequences, primers, and other unwanted sequence from sequence data.
-    usage: qiime cutadapt [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: demux-paired
-        description: Demultiplex paired-end sequence data with barcodes in-sequence.
-        usage: qiime cutadapt demux-paired [OPTIONS]
+      - name: evaluate-contigs
+        description: Evaluate quality of the assembled contigs using metaQUAST.
+        usage: qiime assembly evaluate-contigs [OPTIONS]
         options:
           - names:
-              - --i-seqs
-            argument: ARTIFACT MultiplexedPairedEndBarcodeInSequence
-            description: The paired-end sequences to be demultiplexed. [required]
-          - names:
-              - --m-forward-barcodes-file
-            argument: METADATA
-            description: The sample metadata column listing the per-sample barcodes for the forward reads. [required]
+              - --i-contigs
+            argument: ARTIFACT
+            description: Assembled contigs to be analyzed. [required]
           - names:
-              - --m-forward-barcodes-column
-            argument: COLUMN
-            description: The sample metadata column listing the per-sample barcodes for the forward reads. [required]
+              - --i-reads
+            argument: ARTIFACT
+            description: Original single- or paired-end reads.
           - names:
-              - --m-reverse-barcodes-file
-            argument: METADATA
-            description: The sample metadata column listing the per-sample barcodes for the reverse reads. [optional]
+              - --i-references
+            argument: ARTIFACTS...
+            description: Reference genomes to align the assembled contigs against. [optional]
           - names:
-              - --m-reverse-barcodes-column
-            argument: COLUMN
-            description: The sample metadata column listing the per-sample barcodes for the reverse reads. [optional]
+              - --i-mapped-reads
+            argument: ARTIFACT SampleData[AlignmentMap]
+            description: Reads-to-contigs alignment maps (alternative to 'reads').directly. [optional]
           - names:
-              - --p-forward-cut
+              - --p-min-contig
             argument: INTEGER
-            description: Remove the specified number of bases from the forward sequences.
+            description: Lower threshold for contig length.
           - names:
-              - --p-reverse-cut
+              - --p-threads
             argument: INTEGER
-            description: Remove the specified number of bases from the reverse sequences.
+            description: Maximum number of parallel jobs.
           - names:
-              - --p-anchor-forward-barcode
-              - --p-no-anchor-forward-barcode
+              - --p-k-mer-stats
+              - --p-no-k-mer-stats
             argument: ""
-            description: 'Anchor the forward barcode. The barcode is then expected to occur in full length at the beginning (5'' end) of the forward sequence. Can speed up demultiplexing if used. [default: False]'
+            description: Compute k-mer-based quality metrics (recommended for large genomes). This may significantly increase memory and time consumption on large genomes.
           - names:
-              - --p-anchor-reverse-barcode
-              - --p-no-anchor-reverse-barcode
-            argument: ""
-            description: 'Anchor the reverse barcode. The barcode is then expected to occur in full length at the beginning (5'' end) of the reverse sequence. Can speed up demultiplexing if used. [default: False]'
+              - --p-k-mer-size
+            argument: INTEGER
+            description: Size of k used in k-mer-stats.
           - names:
-              - --p-error-rate
-            argument: PROPORTION
-            description: 'The level of error tolerance, specified as the maximum allowable error rate. [default: 0.1]'
+              - --p-memory-efficient
+              - --p-no-memory-efficient
+            argument: ""
+            description: 'Significantly reduce memory consumption for large genomes. Forces one separate thread per each assembly and each chromosome. [default: False]'
           - names:
-              - --p-batch-size
+              - --p-min-alignment
             argument: INTEGER
-            description: The number of samples cutadapt demultiplexes concurrently.
+            description: Minimum length of alignment (in bp).
           - names:
-              - --p-mixed-orientation
-              - --p-no-mixed-orientation
-            argument: ""
-            description: 'Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file). [default: False]'
+              - --p-min-identity
+            argument: NUMBER
+            description: Minimum percent identity considered as proper alignment.
           - names:
-              - --p-cores
-            argument: NTHREADS
-            description: Number of CPU cores to use.
+              - --p-ambiguity-usage
+            argument: '{none, one, all}'
+            description: 'Way of processing equally good alignments of a contig that are likely repeats. ''none'', skips these alignments. ''one'', takes the very best alignment. ''all'', uses all alignments, but san cause a significant increase of # mismatches.'
           - names:
-              - --p-minimum-length
-            argument: INTEGER
-            description: Discard reads shorter than specified value.
+              - --p-no-icarus
+              - --p-no-no-icarus
+            argument: ""
+            description: Do not draw Icarus visualizations. This option is useful when evaluating large genomes across multiple samples, as this step can be very time-consuming.
           - names:
-              - --o-per-sample-sequences
-            argument: ARTIFACT
-            description: The resulting demultiplexed sequences. [required]
+              - --p-contig-thresholds
+            argument: INTEGERS...
+            description: Range(0, None) List of contig length thresholds.
           - names:
-              - --o-untrimmed-sequences
-            argument: ARTIFACT
-            description: The sequences that were unmatched to barcodes. [required]
+              - --p-ambiguity-score
+            argument: NUMBER
+            description: Range(0.8, 1.0) Score for defining equally good alignments of a
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -1120,52 +1203,80 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: demux-single
-        description: Demultiplex single-end sequence data with barcodes in-sequence.
-        usage: qiime cutadapt demux-single [OPTIONS]
+      - name: generate-reads
+        description: Simulate NGS reads using InSilicoSeq.
+        usage: qiime assembly generate-reads [OPTIONS]
         options:
           - names:
-              - --i-seqs
+              - --i-genomes
             argument: ARTIFACT
-            description: The single-end sequences to be demultiplexed. [required]
+            description: Input genome(s) from which the reads will originate. If the genomes are not provided, they will be fetched from NCBI based on the "ncbi" and "n-genomes-ncbi" parameters. [optional]
           - names:
-              - --m-barcodes-file
-              - --m-barcodes-column
-            argument: METADATA
-            description: The sample metadata column listing the per-sample barcodes. [required]
+              - --p-sample-names
+            argument: TEXT...
+            description: List of sample names that should be generated.
           - names:
-              - --p-cut
+              - --p-n-genomes
             argument: INTEGER
-            description: 'Remove the specified number of bases from the sequences. Bases are removed before demultiplexing. If a positive value is provided, bases are removed from the beginning of the sequences. If a negative value is provided, bases are removed from the end of the sequences. [default: 0]'
+            description: How many genomes will be used for the simulation.
           - names:
-              - --p-anchor-barcode
-              - --p-no-anchor-barcode
-            argument: ""
-            description: Anchor the barcode. The barcode is then expected to occur in full length at the beginning (5' end) of the sequence. Can speed up demultiplexing if used.
+              - --p-ncbi
+            argument: TEXT... '{bacteria, viruses, archaea}'
+            description: Download input genomes from NCBI. Can be bacteria, viruses, archaea or a combination of the three.
           - names:
-              - --p-error-rate
-            argument: PROPORTION
-            description: The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%).
+              - --p-n-genomes-ncbi
+            argument: INTEGERS...
+            description: How many genomes will be downloaded from NCBI.
           - names:
-              - --p-batch-size
+              - --p-abundance
+            argument: '{uniform, halfnormal, exponential, lognormal, zero-inflated-lognormal, off}'
+            description: Abundance distribution.
+          - names:
+              - --p-coverage
+            argument: '{halfnormal, exponential, lognormal, zero-inflated-lognormal, off}'
+            description: Coverage distribution.
+          - names:
+              - --p-n-reads
             argument: INTEGER
-            description: The number of samples cutadapt demultiplexes
+            description: Number of reads to generate.
           - names:
-              - --p-cores
-            argument: NTHREADS
-            description: Number of CPU cores to use.
+              - --p-mode
+            argument: '{kde, basic, perfect}'
+            description: 'Error model. If not specified, using kernel density estimation. [default: ''kde'']'
           - names:
-              - --p-minimum-length
+              - --p-model
+            argument: '{HiSeq, NovaSeq, MiSeq}'
+            description: 'Error model. Use either of the precomputed models when --mode set to ''kde''. [default: ''HiSeq'']'
+          - names:
+              - --p-gc-bias
+              - --p-no-gc-bias
+            argument: ""
+            description: 'If set, may fail to sequence reads with abnormal GC content. [default: False]'
+          - names:
+              - --p-cpus
             argument: INTEGER
-            description: Discard reads shorter than specified value. Note,
+            description: Number of cpus to use.
           - names:
-              - --o-per-sample-sequences
+              - --p-debug
+              - --p-no-debug
+            argument: ""
+            description: 'Enable debug logging. [default: False]'
+          - names:
+              - --p-seed
+            argument: INTEGER
+            description: Seed for all the random number generators.
+          - names:
+              - --o-reads
             argument: ARTIFACT
-            description: The resulting demultiplexed sequences. [required]
+            description: Simulated paired-end reads. [required]
           - names:
-              - --o-untrimmed-sequences
+              - --o-template-genomes
             argument: ARTIFACT
-            description: The sequences that were unmatched to barcodes. [required]
+            description: Genome sequences from which the reads were generated. [required]
+          - names:
+              - --o-abundances
+            argument: ARTIFACT
+            description: Abundances of genomes from which thereads were generated. If "coverage" parameter was set, this table becomes coverage distribution per sample.
           - names:
               - --output-dir
             argument: PATH
@@ -1187,102 +1298,85 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: trim-paired
-        description: Find and remove adapters in demultiplexed paired-end sequences.
-        usage: qiime cutadapt trim-paired [OPTIONS]
+      - name: index-contigs
+        description: Index contigs using Bowtie2.
+        usage: qiime assembly index-contigs [OPTIONS]
         options:
           - names:
-              - --i-demultiplexed-sequences
+              - --i-contigs
             argument: ARTIFACT
-            description: The paired-end sequences to be trimmed. [required]
-          - names:
-              - --p-cores
-            argument: NTHREADS
-            description: Number of CPU cores to use.
-          - names:
-              - --p-adapter-f
-            argument: TEXT...
-            description: Sequence of an adapter ligated to the 3' end. The
-          - names:
-              - --p-front-f
-            argument: TEXT...
-            description: Sequence of an adapter ligated to the 5' end. The
+            description: Contigs to be indexed. [required]
           - names:
-              - --p-anywhere-f
-            argument: TEXT...
-            description: Sequence of an adapter that may be ligated to the
+              - --p-large-index
+              - --p-no-large-index
+            argument: ""
+            description: Force generated index to be 'large', even if ref has fewer than 4 billion nucleotides.
           - names:
-              - --p-adapter-r
-            argument: TEXT...
-            description: Sequence of an adapter ligated to the 3' end. The
+              - --p-debug
+              - --p-no-debug
+            argument: ""
+            description: Use the debug binary; slower, assertions enabled.
           - names:
-              - --p-front-r
-            argument: TEXT...
-            description: Sequence of an adapter ligated to the 5' end. The
+              - --p-sanitized
+              - --p-no-sanitized
+            argument: ""
+            description: 'Use sanitized binary; slower, uses ASan and/or UBSan. [default: False]'
           - names:
-              - --p-anywhere-r
-            argument: TEXT...
-            description: Sequence of an adapter that may be ligated to the
+              - --p-verbose
+              - --p-no-verbose
+            argument: ""
+            description: 'Log the issued command. [default: False]'
           - names:
-              - --p-error-rate
-            argument: PROPORTION
-            description: 'Maximum allowed error rate. [default: 0.1]'
+              - --p-noauto
+              - --p-no-noauto
+            argument: ""
+            description: Disable automatic -p/--bmax/--dcv memory-fitting.
           - names:
-              - --p-indels
-              - --p-no-indels
+              - --p-packed
+              - --p-no-packed
             argument: ""
-            description: Allow insertions or deletions of bases when matching adapters.
+            description: Use packed strings internally; slower, less memory.
           - names:
-              - --p-times
-            argument: INTEGER
-            description: Remove multiple occurrences of an adapter if it is repeated, up to `times` times.
+              - --p-bmax
+            argument: VALUE
+            description: Max bucket sz for blockwise suffix-array builder.
           - names:
-              - --p-overlap
+              - --p-bmaxdivn
             argument: INTEGER
-            description: Require at least `overlap` bases of overlap between read and adapter for an adapter to be found.
-          - names:
-              - --p-match-read-wildcards
-              - --p-no-match-read-wildcards
-            argument: ""
-            description: Interpret IUPAC wildcards (e.g., N) in reads.
-          - names:
-              - --p-match-adapter-wildcards
-              - --p-no-match-adapter-wildcards
-            argument: ""
-            description: Interpret IUPAC wildcards (e.g., N) in adapters.
+            description: Max bucket sz as divisor of ref len.
           - names:
-              - --p-minimum-length
+              - --p-dcv
             argument: INTEGER
-            description: Discard reads shorter than specified value. Note,
+            description: Diff-cover period for blockwise.
           - names:
-              - --p-discard-untrimmed
-              - --p-no-discard-untrimmed
+              - --p-nodc
+              - --p-no-nodc
             argument: ""
-            description: Discard reads in which no adapter was found.
+            description: Disable diff-cover (algorithm becomes quadratic).
           - names:
-              - --p-max-expected-errors
-            argument: NUMBER
-            description: Discard reads that exceed maximum expected erroneous nucleotides.
+              - --p-offrate
+            argument: INTEGER
+            description: SA is sampled every 2^<int> BWT chars.
           - names:
-              - --p-max-n
-            argument: NUMBER
-            description: Discard reads with more than COUNT N bases. If interpreted as a fraction of the read length.
+              - --p-ftabchars
+            argument: INTEGER
+            description: '# of chars consumed in initial lookup.'
           - names:
-              - --p-quality-cutoff-5end
+              - --p-threads
             argument: INTEGER
-            description: Trim nucleotides with Phred score quality lower than threshold from 5 prime end.
+            description: '# of CPUs.'
           - names:
-              - --p-quality-cutoff-3end
+              - --p-seed
             argument: INTEGER
-            description: Trim nucleotides with Phred score quality lower than threshold from 3 prime end.
+            description: Seed for random number generator.
           - names:
-              - --p-quality-base
+              - --p-num-partitions
             argument: INTEGER
-            description: How the Phred score is encoded (33 or 64).
+            description: Range(1, None) The number of partitions to split the contigs into.
           - names:
-              - --o-trimmed-sequences
+              - --o-index
             argument: ARTIFACT
-            description: The resulting trimmed sequences. [required]
+            description: Bowtie2 indices generated for input sequences. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -1292,6 +1386,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -1304,90 +1418,81 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: trim-single
-        description: Find and remove adapters in demultiplexed single-end sequences.
-        usage: qiime cutadapt trim-single [OPTIONS]
+      - name: index-mags
+        description: Index MAGs using Bowtie2.
+        usage: qiime assembly index-mags [OPTIONS]
         options:
           - names:
-              - --i-demultiplexed-sequences
-            argument: ARTIFACT SampleData[SequencesWithQuality]
-            description: The single-end sequences to be trimmed. [required]
+              - --i-mags
+            argument: ARTIFACT
+            description: MAGs to be indexed. [required]
           - names:
-              - --p-cores
-            argument: NTHREADS
-            description: Number of CPU cores to use.
+              - --p-large-index
+              - --p-no-large-index
+            argument: ""
+            description: Force generated index to be 'large', even if ref has fewer than 4 billion nucleotides.
           - names:
-              - --p-adapter
-            argument: TEXT...
-            description: Sequence of an adapter ligated to the 3' end.
+              - --p-debug
+              - --p-no-debug
+            argument: ""
+            description: Use the debug binary; slower, assertions enabled.
           - names:
-              - --p-front
-            argument: TEXT...
-            description: Sequence of an adapter ligated to the 5' end.
+              - --p-sanitized
+              - --p-no-sanitized
+            argument: ""
+            description: 'Use sanitized binary; slower, uses ASan and/or UBSan. [default: False]'
           - names:
-              - --p-anywhere
-            argument: TEXT...
-            description: Sequence of an adapter that may be ligated to the 5' or 3' end.
+              - --p-verbose
+              - --p-no-verbose
+            argument: ""
+            description: 'Log the issued command. [default: False]'
           - names:
-              - --p-error-rate
-            argument: PROPORTION Range(0, 1, inclusive_end=True)
-            description: 'Maximum allowed error rate. [default: 0.1]'
+              - --p-noauto
+              - --p-no-noauto
+            argument: ""
+            description: Disable automatic -p/--bmax/--dcv memory-fitting.
           - names:
-              - --p-indels
-              - --p-no-indels
+              - --p-packed
+              - --p-no-packed
             argument: ""
-            description: Allow insertions or deletions of bases when matching adapters.
+            description: Use packed strings internally; slower, less memory.
           - names:
-              - --p-times
-            argument: INTEGER
-            description: Remove multiple occurrences of an adapter if it is repeated, up to `times` times.
+              - --p-bmax
+            argument: VALUE
+            description: Max bucket sz for blockwise suffix-array builder.
           - names:
-              - --p-overlap
+              - --p-bmaxdivn
             argument: INTEGER
-            description: Require at least `overlap` bases of overlap between read and adapter for an adapter to be found.
-          - names:
-              - --p-match-read-wildcards
-              - --p-no-match-read-wildcards
-            argument: ""
-            description: Interpret IUPAC wildcards (e.g., N) in reads.
-          - names:
-              - --p-match-adapter-wildcards
-              - --p-no-match-adapter-wildcards
-            argument: ""
-            description: Interpret IUPAC wildcards (e.g., N) in adapters.
+            description: Max bucket sz as divisor of ref len.
           - names:
-              - --p-minimum-length
+              - --p-dcv
             argument: INTEGER
-            description: Discard reads shorter than specified value.
+            description: Diff-cover period for blockwise.
           - names:
-              - --p-discard-untrimmed
-              - --p-no-discard-untrimmed
+              - --p-nodc
+              - --p-no-nodc
             argument: ""
-            description: Discard reads in which no adapter was found.
-          - names:
-              - --p-max-expected-errors
-            argument: NUMBER
-            description: Discard reads that exceed maximum expected erroneous nucleotides.
+            description: Disable diff-cover (algorithm becomes quadratic).
           - names:
-              - --p-max-n
-            argument: NUMBER
-            description: Discard reads with more than COUNT N bases.
+              - --p-offrate
+            argument: INTEGER
+            description: SA is sampled every 2^<int> BWT chars.
           - names:
-              - --p-quality-cutoff-5end
+              - --p-ftabchars
             argument: INTEGER
-            description: Trim nucleotides with Phred score quality lower than threshold from 5 prime end.
+            description: '# of chars consumed in initial lookup.'
           - names:
-              - --p-quality-cutoff-3end
+              - --p-threads
             argument: INTEGER
-            description: Trim nucleotides with Phred score quality lower than threshold from 3 prime end.
+            description: '# of CPUs.'
           - names:
-              - --p-quality-base
+              - --p-seed
             argument: INTEGER
-            description: How the Phred score is encoded (33 or 64).
+            description: Seed for random number generator.
           - names:
-              - --o-trimmed-sequences
-            argument: ARTIFACT SampleData[SequencesWithQuality]
-            description: The resulting trimmed sequences. [required]
+              - --o-index
+            argument: ARTIFACT
+            description: Bowtie2 indices generated for input sequences. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -1409,231 +1514,219 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: dada2
-    description: Plugin for sequence quality control with DADA2.
-    usage: qiime dada2 [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: denoise-ccs
-        description: Denoise and dereplicate single-end Pacbio CCS
-        usage: qiime dada2 denoise-ccs [OPTIONS]
+      - name: map-reads-to-contigs
+        description: Map reads to contigs using Bowtie2.
+        usage: qiime assembly map-reads-to-contigs [OPTIONS]
         options:
           - names:
-              - --i-demultiplexed-seqs
-            argument: ARTIFACT SampleData[SequencesWithQuality]
-            description: The single-end demultiplexed PacBio CCS sequences to be denoised. [required]
-          - names:
-              - --p-front
-            argument: TEXT
-            description: Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded. Each read is re-oriented if the reverse complement of the read is a better match to the provided primer sequence. This is recommended for PacBio CCS reads, which come in a random mix of forward and reverse-complement orientations. [required]
+              - --i-indexed-contigs
+            argument: ARTIFACT
+            description: Bowtie 2 indices generated for contigs of interest.
           - names:
-              - --p-adapter
-            argument: TEXT
-            description: Sequence of an adapter ligated to the 3' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded. [required]
+              - --i-reads
+            argument: ARTIFACT
+            description: The paired- or single-end reads from which the contigs were assembled.
           - names:
-              - --p-max-mismatch
+              - --p-skip
             argument: INTEGER
-            description: 'The number of mismatches to tolerate when matching reads to primer sequences - see http://benjjneb.github.io/dada2/ for complete details. [default: 2]'
+            description: Skip (i.e. do not align) the first <int> reads or pairs in the input.
           - names:
-              - --p-indels
-              - --p-no-indels
-            argument: ""
-            description: Allow insertions or deletions of bases when matching adapters. Note that primer matching can be significantly slower, currently about 4x slower
+              - --p-qupto
+            argument: VALUE
+            description: Align the first <int> reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop.
           - names:
-              - --p-trunc-len
+              - --p-trim5
             argument: INTEGER
-            description: 'Position at which sequences should be truncated due to decrease in quality. This truncates the 3'' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed. Note: Since Pacbio CCS sequences were normally with very high quality scores, there is no need to truncate the Pacbio CCS sequences.'
+            description: Trim <int> bases from 5' (left) end of each read before alignment.
           - names:
-              - --p-trim-left
+              - --p-trim3
             argument: INTEGER
-            description: 'Position at which sequences should be trimmed due to low quality. This trims the 5'' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]'
+            description: Trim <int> bases from 3' (right) end of each read before alignment.
           - names:
-              - --p-max-ee
-            argument: NUMBER
-            description: 'Reads with number of expected errors higher than this value will be discarded. [default: 2.0]'
+              - --p-trim-to
+            argument: TEXT
+            description: Trim reads exceeding <int> bases.
           - names:
-              - --p-trunc-q
-            argument: INTEGER
-            description: 'Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]'
+              - --p-phred33
+              - --p-no-phred33
+            argument: ""
+            description: Input qualities are ASCII chars equal to the Phred
           - names:
-              - --p-min-len
+              - --p-phred64
+              - --p-no-phred64
+            argument: ""
+            description: Input qualities are ASCII chars equal to the Phred
+          - names:
+              - --p-mode
+            argument: TEXT Choices('local', 'global')
+            description: bowtie2 alignment settings.
+          - names:
+              - --p-sensitivity
+            argument: TEXT Choices('very-fast', 'fast', 'sensitive', 'very-sensitive')
+            description: bowtie2 alignment sensitivity.
+          - names:
+              - --p-n
             argument: INTEGER
-            description: 'Remove reads with length less than minLen. minLen is enforced after trimming and truncation. For 16S Pacbio CCS, suggest 1000. [default: 20]'
+            description: Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
           - names:
-              - --p-max-len
+              - --p-len
             argument: INTEGER
-            description: 'Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length. For 16S Pacbio CCS, suggest 1600. [default: 0]'
+            description: Sets the length of the seed substrings to align
           - names:
-              - --p-pooling-method
-            argument: TEXT Choices('independent', 'pseudo')
-            description: 'The method used to pool samples for denoising. "independent": Samples are denoised indpendently. "pseudo": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs.'
+              - --p-i
+            argument: TEXT
+            description: Sets a function governing the interval between seed
           - names:
-              - --p-chimera-method
-            argument: TEXT Choices('consensus', 'none', 'pooled')
-            description: 'The method used to remove chimeras. "none": No chimera removal is performed. "pooled": All reads are pooled prior to chimera detection. "consensus": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: ''consensus'']'
+              - --p-n-ceil
+            argument: TEXT
+            description: Sets a function governing the maximum number of
           - names:
-              - --p-min-fold-parent-over-abundance
-            argument: NUMBER
-            description: The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). Suggest 3.5. This parameter has no effect if chimera-method is "none".
+              - --p-dpad
+            argument: INTEGER
+            description: Pads dynamic programming problems by <int> columns on either side to allow gaps.
           - names:
-              - --p-allow-one-off
-              - --p-no-allow-one-off
+              - --p-gbar
+            argument: INTEGER
+            description: Disallow gaps within <int> positions of the beginning or end of the read.
+          - names:
+              - --p-ignore-quals
+              - --p-no-ignore-quals
             argument: ""
-            description: 'Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is True. If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera. [default: False]'
+            description: When calculating a mismatch penalty, always
           - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]'
+              - --p-nofw
+              - --p-no-nofw
+            argument: ""
+            description: If --nofw is specified, bowtie2 will not attempt to
           - names:
-              - --p-n-reads-learn
-            argument: INTEGER
-            description: The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model.
+              - --p-norc
+              - --p-no-norc
+            argument: ""
+            description: If --norc is specified, bowtie2 will not attempt to
           - names:
-              - --p-hashed-feature-ids
-              - --p-no-hashed-feature-ids
+              - --p-no-1mm-upfront
+              - --p-no-no-1mm-upfront
             argument: ""
-            description: 'If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]'
+            description: By default, Bowtie 2 will attempt to find either an
           - names:
-              - --p-retain-all-samples
-              - --p-no-retain-all-samples
+              - --p-end-to-end
+              - --p-no-end-to-end
             argument: ""
-            description: If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table.
+            description: In this mode, Bowtie 2 requires that the entire
           - names:
-              - --o-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting feature table. [required]
+              - --p-local
+              - --p-no-local
+            argument: ""
+            description: In this mode, bowtie2 does not require that the
           - names:
-              - --o-representative-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]
+              - --p-ma
+            argument: INTEGER
+            description: Sets the match bonus.
           - names:
-              - --o-denoising-stats
-            argument: ARTIFACT SampleData[DADA2Stats]
-            description: '[required]'
+              - --p-mp
+            argument: INTEGER
+            description: max penalty for mismatch
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-np
+            argument: INTEGER
+            description: Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --p-rdg
+            argument: TEXT
+            description: Sets the read gap open (<int1>) and extend (<int2>) penalties.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-rfg
+            argument: TEXT
+            description: Sets the reference gap open (<int1>) and extend (<int2>) penalties.
           - names:
-              - --citations
-            argument: ""
-            description: Show citations and exit.
+              - --p-k
+            argument: VALUE
+            description: Report up to <int> alns per read.
           - names:
-              - --help
+              - --p-a
+              - --p-no-a
             argument: ""
-            description: Show this message and exit.
-      - name: denoise-paired
-        description: Denoise and dereplicate paired-end sequences
-        usage: qiime dada2 denoise-paired [OPTIONS]
-        options:
-          - names:
-              - --i-demultiplexed-seqs
-            argument: ARTIFACT SampleData[PairedEndSequencesWithQuality]
-            description: The paired-end demultiplexed sequences to be denoised. [required]
+            description: Report all alignments. Like -k but with no upper
           - names:
-              - --p-trunc-len-f
+              - --p-d
             argument: INTEGER
-            description: Position at which forward read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]
+            description: Up to <int> consecutive seed extension attempts can "fail" before bowtie2 moves on, using the alignments found so far.
           - names:
-              - --p-trunc-len-r
+              - --p-r
             argument: INTEGER
-            description: Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]
+            description: <int> is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
           - names:
-              - --p-trim-left-f
+              - --p-minins
             argument: INTEGER
-            description: 'Position at which forward read sequences should be trimmed due to low quality. This trims the 5'' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]'
+            description: The minimum fragment length for valid paired-end alignments.
           - names:
-              - --p-trim-left-r
+              - --p-maxins
             argument: INTEGER
-            description: 'Position at which reverse read sequences should be trimmed due to low quality. This trims the 5'' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]'
-          - names:
-              - --p-max-ee-f
-            argument: NUMBER
-            description: 'Forward reads with number of expected errors higher than this value will be discarded. [default: 2.0]'
-          - names:
-              - --p-max-ee-r
-            argument: NUMBER
-            description: 'Reverse reads with number of expected errors higher than this value will be discarded. [default: 2.0]'
+            description: The maximum fragment length for valid paired-end alignments.
           - names:
-              - --p-trunc-q
-            argument: INTEGER
-            description: 'Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len-f` or `trunc-len-r` (depending on the direction of the read) it is discarded. [default: 2]'
+              - --p-valid-mate-orientations
+            argument: TEXT Choices('fr', 'rf', 'ff')
+            description: The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand.
           - names:
-              - --p-min-overlap
-            argument: INTEGER
-            description: The minimum length of the overlap required for merging the forward and reverse reads.
+              - --p-no-mixed
+              - --p-no-no-mixed
+            argument: ""
+            description: By default, when bowtie2 cannot find a concordant
           - names:
-              - --p-pooling-method
-            argument: TEXT Choices('independent', 'pseudo')
-            description: 'The method used to pool samples for denoising. "independent": Samples are denoised indpendently. "pseudo": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs.'
+              - --p-no-discordant
+              - --p-no-no-discordant
+            argument: ""
+            description: By default, bowtie2 looks for discordant alignments
           - names:
-              - --p-chimera-method
-            argument: TEXT Choices('consensus', 'none', 'pooled')
-            description: 'The method used to remove chimeras. "none": No chimera removal is performed. "pooled": All reads are pooled prior to chimera detection. "consensus": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: ''consensus'']'
+              - --p-dovetail
+              - --p-no-dovetail
+            argument: ""
+            description: If the mates "dovetail", that is if one mate
           - names:
-              - --p-min-fold-parent-over-abundance
-            argument: NUMBER
-            description: 'The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is "none". [default: 1.0]'
+              - --p-no-contain
+              - --p-no-no-contain
+            argument: ""
+            description: If one mate alignment contains the other, consider
           - names:
-              - --p-allow-one-off
-              - --p-no-allow-one-off
+              - --p-no-overlap
+              - --p-no-no-overlap
             argument: ""
-            description: Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is TrueIf True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera.
+            description: If one mate alignment overlaps the other at all, consider that to be non-concordant.
           - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]'
+              - --p-offrate
+            argument: VALUE
+            description: Override the offrate of the index with <int>.
           - names:
-              - --p-n-reads-learn
+              - --p-threads
             argument: INTEGER
-            description: The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model.
+            description: Launch <int>> parallel search threads.
           - names:
-              - --p-hashed-feature-ids
-              - --p-no-hashed-feature-ids
+              - --p-reorder
+              - --p-no-reorder
             argument: ""
-            description: 'If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]'
+            description: Guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when --threads is set greater than 1.
           - names:
-              - --p-retain-all-samples
-              - --p-no-retain-all-samples
+              - --p-mm
+              - --p-no-mm
             argument: ""
-            description: If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table.
+            description: Use memory-mapped I/O to load the index, rather than typical file I/O.
           - names:
-              - --o-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting feature table. [required]
+              - --p-seed
+            argument: INTEGER
+            description: Use <int> as the seed for pseudo-random number generator.
           - names:
-              - --o-representative-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence, and these sequences will be the joined paired-end sequences. [required]
+              - --p-non-deterministic
+              - --p-no-non-deterministic
+            argument: ""
+            description: If specified, Bowtie 2 re-initializes its
           - names:
-              - --o-denoising-stats
-            argument: ARTIFACT SampleData[DADA2Stats]
-            description: '[required]'
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the contigs into.
+          - names:
+              - --o-alignment-map
+            argument: ARTIFACT
+            description: Reads-to-contigs mapping. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -1644,101 +1737,25 @@ subcommands:
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
           - names:
-              - --citations
+              - --no-recycle
             argument: ""
-            description: Show citations and exit.
-          - names:
-              - --help
-            argument: ""
-            description: Show this message and exit.
-      - name: denoise-pyro
-        description: Denoise and dereplicate single-end pyrosequences
-        usage: qiime dada2 denoise-pyro [OPTIONS]
-        options:
-          - names:
-              - --i-demultiplexed-seqs
-            argument: ARTIFACT SampleData[SequencesWithQuality]
-            description: The single-end demultiplexed pyrosequencing sequences (e.g. 454, IonTorrent) to be denoised.
-          - names:
-              - --p-trunc-len
-            argument: INTEGER
-            description: Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed [required]
-          - names:
-              - --p-trim-left
-            argument: INTEGER
-            description: 'Position at which sequences should be trimmed due to low quality. This trims the 5'' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]'
-          - names:
-              - --p-max-ee
-            argument: NUMBER
-            description: 'Reads with number of expected errors higher than this value will be discarded. [default: 2.0]'
-          - names:
-              - --p-trunc-q
-            argument: INTEGER
-            description: 'Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]'
-          - names:
-              - --p-max-len
-            argument: INTEGER
-            description: 'Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length. [default: 0]'
-          - names:
-              - --p-pooling-method
-            argument: TEXT Choices('independent', 'pseudo')
-            description: 'The method used to pool samples for denoising. "independent": Samples are denoised independently. "pseudo": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs.'
-          - names:
-              - --p-chimera-method
-            argument: TEXT Choices('consensus', 'none', 'pooled')
-            description: 'The method used to remove chimeras. "none": No chimera removal is performed. "pooled": All reads are pooled prior to chimera detection. "consensus": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: ''consensus'']'
-          - names:
-              - --p-min-fold-parent-over-abundance
-            argument: NUMBER
-            description: 'The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is "none". [default: 1.0]'
-          - names:
-              - --p-allow-one-off
-              - --p-no-allow-one-off
-            argument: ""
-            description: 'Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is True. If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera. [default: False]'
-          - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]'
-          - names:
-              - --p-n-reads-learn
-            argument: INTEGER
-            description: The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model.
-          - names:
-              - --p-hashed-feature-ids
-              - --p-no-hashed-feature-ids
-            argument: ""
-            description: 'If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]'
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
           - names:
-              - --p-retain-all-samples
-              - --p-no-retain-all-samples
+              - --parallel
             argument: ""
-            description: If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table.
-          - names:
-              - --o-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting feature table. [required]
-          - names:
-              - --o-representative-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]
-          - names:
-              - --o-denoising-stats
-            argument: ARTIFACT SampleData[DADA2Stats]
-            description: '[required]'
+            description: Execute your action in parallel. This flag will use your default parallel config.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -1751,72 +1768,21 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: denoise-single
-        description: Denoise and dereplicate single-end sequences
-        usage: qiime dada2 denoise-single [OPTIONS]
+      - name: partition-contigs
+        description: Partition contigs
+        usage: qiime assembly partition-contigs [OPTIONS]
         options:
           - names:
-              - --p-trunc-len
-            argument: INTEGER
-            description: Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed [required]
-          - names:
-              - --p-trim-left
-            argument: INTEGER
-            description: 'Position at which sequences should be trimmed due to low quality. This trims the 5'' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]'
-          - names:
-              - --p-max-ee
-            argument: NUMBER
-            description: 'Reads with number of expected errors higher than this value will be discarded. [default: 2.0]'
-          - names:
-              - --p-trunc-q
-            argument: INTEGER
-            description: 'Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]'
-          - names:
-              - --p-pooling-method
-            argument: TEXT Choices('independent', 'pseudo')
-            description: 'The method used to pool samples for denoising. "independent": Samples are denoised independently. "pseudo": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs.'
-          - names:
-              - --p-chimera-method
-            argument: TEXT Choices('consensus', 'none', 'pooled')
-            description: 'The method used to remove chimeras. "none": No chimera removal is performed. "pooled": All reads are pooled prior to chimera detection. "consensus": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: ''consensus'']'
-          - names:
-              - --p-min-fold-parent-over-abundance
-            argument: NUMBER
-            description: 'The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is "none". [default: 1.0]'
-          - names:
-              - --p-allow-one-off
-              - --p-no-allow-one-off
-            argument: ""
-            description: 'Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is True.If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera. [default: False]'
-          - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]'
+              - --i-contigs
+            argument: ARTIFACT
+            description: The contigs to partition. [required]
           - names:
-              - --p-n-reads-learn
+              - --p-num-partitions
             argument: INTEGER
-            description: The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model.
-          - names:
-              - --p-hashed-feature-ids
-              - --p-no-hashed-feature-ids
-            argument: ""
-            description: 'If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]'
-          - names:
-              - --p-retain-all-samples
-              - --p-no-retain-all-samples
-            argument: ""
-            description: If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table.
-          - names:
-              - --o-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting feature table. [required]
-          - names:
-              - --o-representative-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]
+            description: The number of partitions to split the contigs into.
           - names:
-              - --o-denoising-stats
-            argument: ARTIFACT SampleData[DADA2Stats]
+              - --o-partitioned-contigs
+            argument: ARTIFACTS...
             description: '[required]'
           - names:
               - --output-dir
@@ -1839,9 +1805,9 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: deblur
-    description: Plugin for sequence quality control with Deblur.
-    usage: qiime deblur [OPTIONS] COMMAND [ARGS]...
+  - name: composition
+    description: Plugin for compositional data analysis.
+    usage: qiime composition [OPTIONS] COMMAND [ARGS]...
     options:
       - names:
           - --version
@@ -1860,64 +1826,22 @@ subcommands:
         argument: ""
         description: Show this message and exit.
     subcommands:
-      - name: denoise-16S
-        description: Deblur sequences using a 16S positive filter.
-        usage: qiime deblur denoise-16S [OPTIONS]
+      - name: add-pseudocount
+        description: Add pseudocount to table.
+        usage: qiime composition add-pseudocount [OPTIONS]
         options:
           - names:
-              - --p-trim-length
-            argument: INTEGER
-            description: Sequence trim length, specify -1 to disable trimming. [required]
-          - names:
-              - --p-sample-stats
-              - --p-no-sample-stats
-            argument: ""
-            description: 'If true, gather stats per sample. [default: False]'
-          - names:
-              - --p-mean-error
-            argument: NUMBER
-            description: 'The mean per nucleotide error, used for original sequence estimate. [default: 0.005]'
-          - names:
-              - --p-indel-prob
-            argument: NUMBER
-            description: 'Insertion/deletion (indel) probability (same for N indels). [default: 0.01]'
-          - names:
-              - --p-indel-max
-            argument: INTEGER
-            description: 'Maximum number of insertion/deletions. [default: 3]'
-          - names:
-              - --p-min-reads
-            argument: INTEGER
-            description: 'Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]'
-          - names:
-              - --p-min-size
-            argument: INTEGER
-            description: 'In each sample, discard all features with an abundance less than min-size. [default: 2]'
-          - names:
-              - --p-jobs-to-start
-            argument: NTHREADS
-            description: Number of jobs to start (if to run in parallel).
-          - names:
-              - --p-hashed-feature-ids
-              - --p-no-hashed-feature-ids
-            argument: ""
-            description: 'If true, hash the feature IDs. [default: True]'
-          - names:
-              - --p-left-trim-len
-            argument: INTEGER
-            description: Sequence trimming from the 5' end. A value of 0 will
-          - names:
-              - --o-table
+              - --i-table
             argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting denoised feature table. [required]
+            description: The feature table to which pseudocounts should be added. [required]
           - names:
-              - --o-representative-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The resulting feature sequences. [required]
+              - --p-pseudocount
+            argument: INTEGER
+            description: The value to add to all counts in the feature table.
           - names:
-              - --o-stats
-            argument: ARTIFACT
-            description: Per-sample stats if requested.
+              - --o-composition-table
+            argument: ARTIFACT FeatureTable[Composition]
+            description: The resulting feature table. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -1939,72 +1863,36 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: denoise-other
-        description: Deblur sequences using a user-specified positive filter.
-        usage: qiime deblur denoise-other [OPTIONS]
+      - name: ancom
+        description: Apply ANCOM to identify features that differ in abundance.
+        usage: qiime composition ancom [OPTIONS]
         options:
           - names:
-              - --i-demultiplexed-seqs
-            argument: ""
-            description: ARTIFACT SampleData[SequencesWithQuality |
+              - --i-table
+            argument: ARTIFACT FeatureTable[Composition]
+            description: The feature table to be used for ANCOM computation.
           - names:
-              - --i-reference-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Positive filtering database. Keep all sequences aligning to these sequences. [required]
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: The categorical sample metadata column to test for differential abundance across. [required]
           - names:
-              - --p-trim-length
-            argument: INTEGER
-            description: Sequence trim length, specify -1 to disable trimming. [required]
+              - --p-transform-function
+            argument: TEXT Choices('sqrt', 'log', 'clr')
+            description: 'The method applied to transform feature values before generating volcano plots. [default: ''clr'']'
           - names:
-              - --p-sample-stats
-              - --p-no-sample-stats
-            argument: ""
-            description: 'If true, gather stats per sample. [default: False]'
-          - names:
-              - --p-mean-error
-            argument: NUMBER
-            description: 'The mean per nucleotide error, used for original sequence estimate. [default: 0.005]'
-          - names:
-              - --p-indel-prob
-            argument: NUMBER
-            description: 'Insertion/deletion (indel) probability (same for N indels). [default: 0.01]'
-          - names:
-              - --p-indel-max
-            argument: INTEGER
-            description: 'Maximum number of insertion/deletions. [default: 3]'
-          - names:
-              - --p-min-reads
-            argument: INTEGER
-            description: 'Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]'
-          - names:
-              - --p-min-size
-            argument: INTEGER
-            description: 'In each sample, discard all features with an abundance less than min-size. [default: 2]'
-          - names:
-              - --p-jobs-to-start
-            argument: NTHREADS
-            description: Number of jobs to start (if to run in parallel).
+              - --p-difference-function
+            argument: TEXT Choices('mean_difference', 'f_statistic')
+            description: The method applied to visualize fold difference in feature abundances across groups for volcano plots.
           - names:
-              - --p-hashed-feature-ids
-              - --p-no-hashed-feature-ids
+              - --p-filter-missing
+              - --p-no-filter-missing
             argument: ""
-            description: 'If true, hash the feature IDs. [default: True]'
-          - names:
-              - --p-left-trim-len
-            argument: INTEGER
-            description: Sequence trimming from the 5' end. A value of 0 will
-          - names:
-              - --o-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting denoised feature table. [required]
-          - names:
-              - --o-representative-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The resulting feature sequences. [required]
+            description: 'If True, samples with missing metadata values will be filtered from the table prior to analysis. If False, an error will be raised if there are any missing metadata values. [default: False]'
           - names:
-              - --o-stats
-            argument: ARTIFACT
-            description: Per-sample stats if requested. [required]
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -2026,18 +1914,60 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: visualize-stats
-        description: Visualize Deblur stats per sample.
-        usage: qiime deblur visualize-stats [OPTIONS]
+      - name: ancombc
+        description: Analysis of Composition of Microbiomes with Bias Correction
+        usage: qiime composition ancombc [OPTIONS]
         options:
           - names:
-              - --i-deblur-stats
-            argument: ARTIFACT
-            description: DeblurStats Summary statistics of the Deblur process. [required]
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table to be used for ANCOM-BC computation. [required]
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata.
+          - names:
+              - --p-formula
+            argument: TEXT
+            description: How the microbial absolute abundances for each taxon depend on the variables within the `metadata`.
+          - names:
+              - --p-p-adj-method
+            argument: TEXT
+            description: "Method to adjust p-values. Choices('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')"
+          - names:
+              - --p-prv-cut
+            argument: NUMBER
+            description: 'A numerical fraction between 0-1. Taxa with prevalences less than this value will be excluded from the analysis. [default: 0.1]'
+          - names:
+              - --p-lib-cut
+            argument: INTEGER
+            description: A numerical threshold for filtering samples based on library sizes. Samples with library sizes less than this value will be excluded from the analysis.
+
+          - names:
+              - --p-reference-levels
+            argument: TEXT...
+            description: Define the reference level(s) to be used for categorical columns found in the `formula`.
+          - names:
+              - --p-tol
+            argument: NUMBER
+            description: 'The iteration convergence tolerance for the E-M algorithm. [default: 1e-05]'
+          - names:
+              - --p-max-iter
+            argument: INTEGER
+            description: 'The maximum number of iterations for the E-M algorithm. [default: 100]'
+          - names:
+              - --p-conserve
+              - --p-no-conserve
+            argument: ""
+            description: Whether to use a conservative variance estimator for the test statistic. It is recommended if the sample size is small and/or the number of differentially abundant taxa is believed to be large.
+          - names:
+              - --p-alpha
+            argument: NUMBER
+            description: 'Level of significance. [default: 0.05]'
+          - names:
+              - --o-differentials
+            argument: ARTIFACT FeatureData[DifferentialAbundance]
+            description: The calculated per-feature differentials. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -2059,68 +1989,54 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: demux
-    description: Plugin for demultiplexing & viewing sequence quality.
-    usage: qiime demux [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: emp-paired
-        description: Demultiplex paired-end sequence data generated with the EMP protocol.
-        usage: qiime demux emp-paired [OPTIONS]
+      - name: da-barplot
+        description: Differential abundance bar plots
+        usage: qiime composition da-barplot [OPTIONS]
         options:
           - names:
-              - --i-seqs
-            argument: ARTIFACT EMPPairedEndSequences
-            description: The paired-end sequences to be demultiplexed.
+              - --i-data
+            argument: ARTIFACT FeatureData[DifferentialAbundance]
+            description: The ANCOM-BC output to be plotted. [required]
           - names:
-              - --m-barcodes-file
-              - --m-barcodes-column
-            argument: METADATA
-            description: The sample metadata column containing the per-sample barcodes. [required]
+              - --p-effect-size-label
+            argument: TEXT
+            description: 'Label for effect sizes in `data`. [default: ''lfc'']'
           - names:
-              - --p-golay-error-correction
-              - --p-no-golay-error-correction
-            argument: ""
-            description: 'Perform 12nt Golay error correction on the barcode reads. [default: True]'
+              - --p-feature-id-label
+            argument: TEXT
+            description: 'Label for feature ids in `data`. [default: ''id'']'
           - names:
-              - --p-rev-comp-barcodes
-              - --p-no-rev-comp-barcodes
-            argument: ""
-            description: If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing.
+              - --p-error-label
+            argument: TEXT
+            description: Label for effect size errors in `data`.
           - names:
-              - --p-rev-comp-mapping-barcodes
-              - --p-no-rev-comp-mapping-barcodes
-            argument: ""
-            description: 'If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]'
+              - --p-significance-label
+            argument: TEXT
+            description: Label for statistical significance level in `data`.
           - names:
-              - --p-ignore-description-mismatch
-              - --p-no-ignore-description-mismatch
-            argument: ""
-            description: 'If enabled, ignore mismatches in sequence record description fields. [default: False]'
+              - --p-significance-threshold
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: Exclude features with statistical significance level greater (i.e., less significant) than this threshold.
           - names:
-              - --o-error-correction-details
-            argument: ARTIFACT ErrorCorrectionDetails
-            description: Detail about the barcode error corrections. [required]
+              - --p-level-delimiter
+            argument: TEXT
+            description: If feature ids encode hierarchical information, split the levels when generating feature labels in the visualization using this delimiter. [optional]
           - names:
-              - --o-per-sample-sequences
-            argument: ARTIFACT
-            description: SampleData[PairedEndSequencesWithQuality]
+              - --p-label-limit
+            argument: INTEGER
+            description: Set the maximum length that will be viewable for axis labels. You can set this parameter if your axis labels are being cut off. [optional]
+          - names:
+              - --p-effect-size-threshold
+            argument: NUMBER
+            description: Exclude features with an absolute value of effect size less than this threshold.
+          - names:
+              - --m-feature-ids-file
+            argument: METADATA...
+            description: Exclude features if their ids are not included in this index.
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -2142,43 +2058,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: emp-single
-        description: Demultiplex sequence data generated with the EMP protocol.
-        usage: qiime demux emp-single [OPTIONS]
+      - name: tabulate
+        description: View tabular output from ANCOM-BC.
+        usage: qiime composition tabulate [OPTIONS]
         options:
           - names:
-              - --m-barcodes-file
-              - --m-barcodes-column
-            argument: METADATA
-            description: The sample metadata column containing the per-sample barcodes. [required]
-          - names:
-              - --p-golay-error-correction
-              - --p-no-golay-error-correction
-            argument: ""
-            description: 'Perform 12nt Golay error correction on the barcode reads. [default: True]'
-          - names:
-              - --p-rev-comp-barcodes
-              - --p-no-rev-comp-barcodes
-            argument: ""
-            description: If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing.
-          - names:
-              - --p-rev-comp-mapping-barcodes
-              - --p-no-rev-comp-mapping-barcodes
-            argument: ""
-            description: 'If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]'
-          - names:
-              - --p-ignore-description-mismatch
-              - --p-no-ignore-description-mismatch
-            argument: ""
-            description: 'If enabled, ignore mismatches in sequence record description fields. [default: False]'
-          - names:
-              - --o-per-sample-sequences
-            argument: ARTIFACT SampleData[SequencesWithQuality]
-            description: The resulting demultiplexed sequences. [required]
+              - --i-data
+            argument: ARTIFACT FeatureData[DifferentialAbundance]
+            description: The ANCOM-BC output to be tabulated. [required]
           - names:
-              - --o-error-correction-details
-            argument: ARTIFACT ErrorCorrectionDetails
-            description: Detail about the barcode error corrections. [required]
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -2200,138 +2091,98 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-samples
-        description: Filter samples out of demultiplexed data.
-        usage: qiime demux filter-samples [OPTIONS]
-        options:
-          - names:
-            - --i-demux
-            argument: ARTIFACT
-            description: The demultiplexed data from which samples should be filtered. [required]
-          - names:
-            - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata indicating which sample ids to filter. [required]
-          - names:
-              - --p-where
-            argument: TEXT
-            description: Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]
-          - names:
-              - --p-exclude-ids
-              - --p-no-exclude-ids
-            argument: ""
-            description: 'Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]'
-          - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+  - name: cutadapt
+    description: Plugin for removing adapter sequences, primers, and other unwanted sequence from sequence data.
+    usage: qiime cutadapt [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: demux-paired
+        description: Demultiplex paired-end sequence data with barcodes in-sequence.
+        usage: qiime cutadapt demux-paired [OPTIONS]
+        options:
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --i-seqs
+            argument: ARTIFACT MultiplexedPairedEndBarcodeInSequence
+            description: The paired-end sequences to be demultiplexed. [required]
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --m-forward-barcodes-file
+            argument: METADATA
+            description: The sample metadata column listing the per-sample barcodes for the forward reads. [required]
           - names:
-              - --citations
-            argument: ""
-            description: Show citations and exit.
+              - --m-forward-barcodes-column
+            argument: COLUMN
+            description: The sample metadata column listing the per-sample barcodes for the forward reads. [required]
           - names:
-              - --help
-            argument: ""
-            description: Show this message and exit.
-      - name: partition-samples-paired
-        description: Split demultiplexed sequence data into partitions.
-        usage: qiime demux partition-samples-paired [OPTIONS]
-        options:
+              - --m-reverse-barcodes-file
+            argument: METADATA
+            description: The sample metadata column listing the per-sample barcodes for the reverse reads. [optional]
           - names:
-              - --i-demux
-            argument: ARTIFACT SampleData[PairedEndSequencesWithQuality]
-            description: The demultiplexed sequences to partition. [required]
+              - --m-reverse-barcodes-column
+            argument: COLUMN
+            description: The sample metadata column listing the per-sample barcodes for the reverse reads. [optional]
           - names:
-              - --p-num-partitions
+              - --p-forward-cut
             argument: INTEGER
-            description: The number of partitions to split the demultiplexed
-          - names:
-              - --o-partitioned-demux
-            argument: ARTIFACTS...
-            description: Collection[SampleData[PairedEndSequencesWithQuality]]
-          - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
-          - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+            description: Remove the specified number of bases from the forward sequences.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-reverse-cut
+            argument: INTEGER
+            description: Remove the specified number of bases from the reverse sequences.
           - names:
-              - --citations
+              - --p-anchor-forward-barcode
+              - --p-no-anchor-forward-barcode
             argument: ""
-            description: Show citations and exit.
+            description: 'Anchor the forward barcode. The barcode is then expected to occur in full length at the beginning (5'' end) of the forward sequence. Can speed up demultiplexing if used. [default: False]'
           - names:
-              - --help
+              - --p-anchor-reverse-barcode
+              - --p-no-anchor-reverse-barcode
             argument: ""
-            description: Show this message and exit.
-      - name: partition-samples-single
-        description: Split demultiplexed sequence data into partitions.
-        usage: qiime demux partition-samples-single [OPTIONS]
-        options:
+            description: 'Anchor the reverse barcode. The barcode is then expected to occur in full length at the beginning (5'' end) of the reverse sequence. Can speed up demultiplexing if used. [default: False]'
           - names:
-              - --i-demux
-            argument: ARTIFACT SampleData[SequencesWithQuality]
-            description: The demultiplexed sequences to partition. [required]
+              - --p-error-rate
+            argument: PROPORTION
+            description: 'The level of error tolerance, specified as the maximum allowable error rate. [default: 0.1]'
           - names:
-              - --p-num-partitions
+              - --p-batch-size
             argument: INTEGER
-            description: The number of partitions to split the demultiplexed
-          - names:
-              - --o-partitioned-demux
-            argument: ARTIFACTS...
-            description: Collection[SampleData[SequencesWithQuality]]
-          - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
-          - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+            description: The number of samples cutadapt demultiplexes concurrently.
           - names:
-              - --citations
+              - --p-mixed-orientation
+              - --p-no-mixed-orientation
             argument: ""
-            description: Show citations and exit.
+            description: 'Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file). [default: False]'
           - names:
-              - --help
-            argument: ""
-            description: Show this message and exit.
-      - name: subsample-paired
-        description: Subsample paired-end sequences without replacement.
-        usage: qiime demux subsample-paired [OPTIONS]
-        options:
+              - --p-cores
+            argument: NTHREADS
+            description: Number of CPU cores to use.
           - names:
-              - --i-sequences
-            argument: ARTIFACT SampleData[PairedEndSequencesWithQuality]
-            description: The demultiplexed sequences to be subsampled.
+              - --p-minimum-length
+            argument: INTEGER
+            description: Discard reads shorter than specified value.
           - names:
-              - --p-fraction
-            argument: PROPORTION Range(0, 1, inclusive_start=False)
-            description: The fraction of sequences to retain in subsample.
+              - --o-per-sample-sequences
+            argument: ARTIFACT
+            description: The resulting demultiplexed sequences. [required]
           - names:
-              - --o-subsampled-sequences
+              - --o-untrimmed-sequences
             argument: ARTIFACT
-            description: SampleData[PairedEndSequencesWithQuality]
+            description: The sequences that were unmatched to barcodes. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -2353,51 +2204,52 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: subsample-single
-        description: Subsample single-end sequences without replacement.
-        usage: qiime demux subsample-single [OPTIONS]
+      - name: demux-single
+        description: Demultiplex single-end sequence data with barcodes in-sequence.
+        usage: qiime cutadapt demux-single [OPTIONS]
         options:
           - names:
-              - --p-fraction
-            argument: PROPORTION Range(0, 1, inclusive_start=False)
-            description: The fraction of sequences to retain in subsample.
+              - --i-seqs
+            argument: ARTIFACT
+            description: The single-end sequences to be demultiplexed. [required]
           - names:
-              - --o-subsampled-sequences
-            argument: ARTIFACT SampleData[SequencesWithQuality]
-            description: The subsampled sequences. [required]
+              - --m-barcodes-file
+              - --m-barcodes-column
+            argument: METADATA
+            description: The sample metadata column listing the per-sample barcodes. [required]
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-cut
+            argument: INTEGER
+            description: 'Remove the specified number of bases from the sequences. Bases are removed before demultiplexing. If a positive value is provided, bases are removed from the beginning of the sequences. If a negative value is provided, bases are removed from the end of the sequences. [default: 0]'
           - names:
-              - --verbose
-              - --quiet
+              - --p-anchor-barcode
+              - --p-no-anchor-barcode
             argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+            description: Anchor the barcode. The barcode is then expected to occur in full length at the beginning (5' end) of the sequence. Can speed up demultiplexing if used.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-error-rate
+            argument: PROPORTION
+            description: The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%).
           - names:
-              - --citations
-            argument: ""
-            description: Show citations and exit.
+              - --p-batch-size
+            argument: INTEGER
+            description: The number of samples cutadapt demultiplexes
           - names:
-              - --help
-            argument: ""
-            description: Show this message and exit.
-      - name: summarize
-        description: Summarize counts per sample.
-        usage: qiime demux summarize [OPTIONS]
-        options:
+              - --p-cores
+            argument: NTHREADS
+            description: Number of CPU cores to use.
           - names:
-              - --p-n
+              - --p-minimum-length
             argument: INTEGER
-            description: The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences.
+            description: Discard reads shorter than specified value. Note,
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-per-sample-sequences
+            argument: ARTIFACT
+            description: The resulting demultiplexed sequences. [required]
+          - names:
+              - --o-untrimmed-sequences
+            argument: ARTIFACT
+            description: The sequences that were unmatched to barcodes. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -2419,84 +2271,102 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: tabulate-read-counts
-        description: Tabulate counts per sample
-        usage: qiime demux tabulate-read-counts [OPTIONS]
+      - name: trim-paired
+        description: Find and remove adapters in demultiplexed paired-end sequences.
+        usage: qiime cutadapt trim-paired [OPTIONS]
         options:
           - names:
-              - --o-counts
+              - --i-demultiplexed-sequences
             argument: ARTIFACT
-            description: ImmutableMetadata [required]
+            description: The paired-end sequences to be trimmed. [required]
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-cores
+            argument: NTHREADS
+            description: Number of CPU cores to use.
           - names:
-              - --verbose
-              - --quiet
+              - --p-adapter-f
+            argument: TEXT...
+            description: Sequence of an adapter ligated to the 3' end. The
+          - names:
+              - --p-front-f
+            argument: TEXT...
+            description: Sequence of an adapter ligated to the 5' end. The
+          - names:
+              - --p-anywhere-f
+            argument: TEXT...
+            description: Sequence of an adapter that may be ligated to the
+          - names:
+              - --p-adapter-r
+            argument: TEXT...
+            description: Sequence of an adapter ligated to the 3' end. The
+          - names:
+              - --p-front-r
+            argument: TEXT...
+            description: Sequence of an adapter ligated to the 5' end. The
+          - names:
+              - --p-anywhere-r
+            argument: TEXT...
+            description: Sequence of an adapter that may be ligated to the
+          - names:
+              - --p-error-rate
+            argument: PROPORTION
+            description: 'Maximum allowed error rate. [default: 0.1]'
+          - names:
+              - --p-indels
+              - --p-no-indels
             argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+            description: Allow insertions or deletions of bases when matching adapters.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-times
+            argument: INTEGER
+            description: Remove multiple occurrences of an adapter if it is repeated, up to `times` times.
           - names:
-              - --citations
+              - --p-overlap
+            argument: INTEGER
+            description: Require at least `overlap` bases of overlap between read and adapter for an adapter to be found.
+          - names:
+              - --p-match-read-wildcards
+              - --p-no-match-read-wildcards
             argument: ""
-            description: Show citations and exit.
+            description: Interpret IUPAC wildcards (e.g., N) in reads.
           - names:
-              - --help
+              - --p-match-adapter-wildcards
+              - --p-no-match-adapter-wildcards
             argument: ""
-            description: Show this message and exit.
-  - name: diversity
-    description: Plugin for exploring community diversity.
-    usage: qiime diversity [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: adonis
-        description: adonis PERMANOVA test for beta group significance
-        usage: qiime diversity adonis [OPTIONS]
-        options:
+            description: Interpret IUPAC wildcards (e.g., N) in adapters.
           - names:
-              - --i-distance-matrix
-            argument: ARTIFACT
-            description: Matrix of distances between pairs of samples. [required]
+              - --p-minimum-length
+            argument: INTEGER
+            description: Discard reads shorter than specified value. Note,
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata containing formula terms. [required]
+              - --p-discard-untrimmed
+              - --p-no-discard-untrimmed
+            argument: ""
+            description: Discard reads in which no adapter was found.
           - names:
-              - --p-formula
-            argument: TEXT
-            description: Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula "treatment+block" would test whether the input distance matrix partitions based on "treatment" and "block" sample metadata. The formula "treatment*block" would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]
+              - --p-max-expected-errors
+            argument: NUMBER
+            description: Discard reads that exceed maximum expected erroneous nucleotides.
           - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: Number of parallel processes to run
+              - --p-max-n
+            argument: NUMBER
+            description: Discard reads with more than COUNT N bases. If interpreted as a fraction of the read length.
           - names:
-              - --p-permutations
+              - --p-quality-cutoff-5end
             argument: INTEGER
-            description: The number of permutations to be run when computing
+            description: Trim nucleotides with Phred score quality lower than threshold from 5 prime end.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --p-quality-cutoff-3end
+            argument: INTEGER
+            description: Trim nucleotides with Phred score quality lower than threshold from 3 prime end.
+          - names:
+              - --p-quality-base
+            argument: INTEGER
+            description: How the Phred score is encoded (33 or 64).
+          - names:
+              - --o-trimmed-sequences
+            argument: ARTIFACT
+            description: The resulting trimmed sequences. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -2518,88 +2388,90 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: alpha
-        description: Alpha diversity
-        usage: qiime diversity alpha [OPTIONS]
+      - name: trim-single
+        description: Find and remove adapters in demultiplexed single-end sequences.
+        usage: qiime cutadapt trim-single [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable
-            description: The feature table containing the samples for which
-          - names:
-              - --i-table
-            argument: ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence
-            description: The feature table containing the samples for which
+              - --i-demultiplexed-sequences
+            argument: ARTIFACT SampleData[SequencesWithQuality]
+            description: The single-end sequences to be trimmed. [required]
           - names:
-              - --o-alpha-diversity
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector containing per-sample alpha diversities.
+              - --p-cores
+            argument: NTHREADS
+            description: Number of CPU cores to use.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-adapter
+            argument: TEXT...
+            description: Sequence of an adapter ligated to the 3' end.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --p-front
+            argument: TEXT...
+            description: Sequence of an adapter ligated to the 5' end.
           - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+              - --p-anywhere
+            argument: TEXT...
+            description: Sequence of an adapter that may be ligated to the 5' or 3' end.
           - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+              - --p-error-rate
+            argument: PROPORTION Range(0, 1, inclusive_end=True)
+            description: 'Maximum allowed error rate. [default: 0.1]'
           - names:
-              - --parallel
+              - --p-indels
+              - --p-no-indels
             argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
+            description: Allow insertions or deletions of bases when matching adapters.
           - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
+              - --p-times
+            argument: INTEGER
+            description: Remove multiple occurrences of an adapter if it is repeated, up to `times` times.
           - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+              - --p-overlap
+            argument: INTEGER
+            description: Require at least `overlap` bases of overlap between read and adapter for an adapter to be found.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-match-read-wildcards
+              - --p-no-match-read-wildcards
+            argument: ""
+            description: Interpret IUPAC wildcards (e.g., N) in reads.
           - names:
-              - --citations
+              - --p-match-adapter-wildcards
+              - --p-no-match-adapter-wildcards
             argument: ""
-            description: Show citations and exit.
+            description: Interpret IUPAC wildcards (e.g., N) in adapters.
           - names:
-              - --help
+              - --p-minimum-length
+            argument: INTEGER
+            description: Discard reads shorter than specified value.
+          - names:
+              - --p-discard-untrimmed
+              - --p-no-discard-untrimmed
             argument: ""
-            description: Show this message and exit.
-      - name: alpha-correlation
-        description: Alpha diversity correlation
-        usage: qiime diversity alpha-correlation [OPTIONS]
-        options:
+            description: Discard reads in which no adapter was found.
           - names:
-              - --i-alpha-diversity
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector of alpha diversity values by sample. [required]
+              - --p-max-expected-errors
+            argument: NUMBER
+            description: Discard reads that exceed maximum expected erroneous nucleotides.
           - names:
-              - --p-method
-            argument: TEXT Choices('spearman', 'pearson')
-            description: The correlation test to be applied.
+              - --p-max-n
+            argument: NUMBER
+            description: Discard reads with more than COUNT N bases.
           - names:
-              - --p-intersect-ids
-              - --p-no-intersect-ids
-            argument: ""
-            description: 'If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs. [default: False]'
+              - --p-quality-cutoff-5end
+            argument: INTEGER
+            description: Trim nucleotides with Phred score quality lower than threshold from 5 prime end.
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata.
+              - --p-quality-cutoff-3end
+            argument: INTEGER
+            description: Trim nucleotides with Phred score quality lower than threshold from 3 prime end.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --p-quality-base
+            argument: INTEGER
+            description: How the Phred score is encoded (33 or 64).
+          - names:
+              - --o-trimmed-sequences
+            argument: ARTIFACT SampleData[SequencesWithQuality]
+            description: The resulting trimmed sequences. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -2621,22 +2493,4890 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: alpha-group-significance
-        description: Alpha diversity comparisons
-        usage: qiime diversity alpha-group-significance [OPTIONS]
-        options:
-          - names:
-              - --i-alpha-diversity
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector of alpha diversity values by sample. [required]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata. [required]
+  - name: dada2
+    description: Plugin for sequence quality control with DADA2.
+    usage: qiime dada2 [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: denoise-ccs
+        description: Denoise and dereplicate single-end Pacbio CCS
+        usage: qiime dada2 denoise-ccs [OPTIONS]
+        options:
+          - names:
+              - --i-demultiplexed-seqs
+            argument: ARTIFACT SampleData[SequencesWithQuality]
+            description: The single-end demultiplexed PacBio CCS sequences to be denoised. [required]
+          - names:
+              - --p-front
+            argument: TEXT
+            description: Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded. Each read is re-oriented if the reverse complement of the read is a better match to the provided primer sequence. This is recommended for PacBio CCS reads, which come in a random mix of forward and reverse-complement orientations. [required]
+          - names:
+              - --p-adapter
+            argument: TEXT
+            description: Sequence of an adapter ligated to the 3' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded. [required]
+          - names:
+              - --p-max-mismatch
+            argument: INTEGER
+            description: 'The number of mismatches to tolerate when matching reads to primer sequences - see http://benjjneb.github.io/dada2/ for complete details. [default: 2]'
+          - names:
+              - --p-indels
+              - --p-no-indels
+            argument: ""
+            description: Allow insertions or deletions of bases when matching adapters. Note that primer matching can be significantly slower, currently about 4x slower
+          - names:
+              - --p-trunc-len
+            argument: INTEGER
+            description: 'Position at which sequences should be truncated due to decrease in quality. This truncates the 3'' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed. Note: Since Pacbio CCS sequences were normally with very high quality scores, there is no need to truncate the Pacbio CCS sequences.'
+          - names:
+              - --p-trim-left
+            argument: INTEGER
+            description: 'Position at which sequences should be trimmed due to low quality. This trims the 5'' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]'
+          - names:
+              - --p-max-ee
+            argument: NUMBER
+            description: 'Reads with number of expected errors higher than this value will be discarded. [default: 2.0]'
+          - names:
+              - --p-trunc-q
+            argument: INTEGER
+            description: 'Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]'
+          - names:
+              - --p-min-len
+            argument: INTEGER
+            description: 'Remove reads with length less than minLen. minLen is enforced after trimming and truncation. For 16S Pacbio CCS, suggest 1000. [default: 20]'
+          - names:
+              - --p-max-len
+            argument: INTEGER
+            description: 'Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length. For 16S Pacbio CCS, suggest 1600. [default: 0]'
+          - names:
+              - --p-pooling-method
+            argument: TEXT Choices('independent', 'pseudo')
+            description: 'The method used to pool samples for denoising. "independent": Samples are denoised indpendently. "pseudo": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs.'
+          - names:
+              - --p-chimera-method
+            argument: TEXT Choices('consensus', 'none', 'pooled')
+            description: 'The method used to remove chimeras. "none": No chimera removal is performed. "pooled": All reads are pooled prior to chimera detection. "consensus": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: ''consensus'']'
+          - names:
+              - --p-min-fold-parent-over-abundance
+            argument: NUMBER
+            description: The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). Suggest 3.5. This parameter has no effect if chimera-method is "none".
+          - names:
+              - --p-allow-one-off
+              - --p-no-allow-one-off
+            argument: ""
+            description: 'Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is True. If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera. [default: False]'
+          - names:
+              - --p-n-threads
+            argument: NTHREADS
+            description: 'The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]'
+          - names:
+              - --p-n-reads-learn
+            argument: INTEGER
+            description: The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model.
+          - names:
+              - --p-hashed-feature-ids
+              - --p-no-hashed-feature-ids
+            argument: ""
+            description: 'If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]'
+          - names:
+              - --p-retain-all-samples
+              - --p-no-retain-all-samples
+            argument: ""
+            description: If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table.
+          - names:
+              - --o-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting feature table. [required]
+          - names:
+              - --o-representative-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]
+          - names:
+              - --o-denoising-stats
+            argument: ARTIFACT SampleData[DADA2Stats]
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: denoise-paired
+        description: Denoise and dereplicate paired-end sequences
+        usage: qiime dada2 denoise-paired [OPTIONS]
+        options:
+          - names:
+              - --i-demultiplexed-seqs
+            argument: ARTIFACT SampleData[PairedEndSequencesWithQuality]
+            description: The paired-end demultiplexed sequences to be denoised. [required]
+          - names:
+              - --p-trunc-len-f
+            argument: INTEGER
+            description: Position at which forward read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]
+          - names:
+              - --p-trunc-len-r
+            argument: INTEGER
+            description: Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]
+          - names:
+              - --p-trim-left-f
+            argument: INTEGER
+            description: 'Position at which forward read sequences should be trimmed due to low quality. This trims the 5'' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]'
+          - names:
+              - --p-trim-left-r
+            argument: INTEGER
+            description: 'Position at which reverse read sequences should be trimmed due to low quality. This trims the 5'' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]'
+          - names:
+              - --p-max-ee-f
+            argument: NUMBER
+            description: 'Forward reads with number of expected errors higher than this value will be discarded. [default: 2.0]'
+          - names:
+              - --p-max-ee-r
+            argument: NUMBER
+            description: 'Reverse reads with number of expected errors higher than this value will be discarded. [default: 2.0]'
+          - names:
+              - --p-trunc-q
+            argument: INTEGER
+            description: 'Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len-f` or `trunc-len-r` (depending on the direction of the read) it is discarded. [default: 2]'
+          - names:
+              - --p-min-overlap
+            argument: INTEGER
+            description: The minimum length of the overlap required for merging the forward and reverse reads.
+          - names:
+              - --p-pooling-method
+            argument: TEXT Choices('independent', 'pseudo')
+            description: 'The method used to pool samples for denoising. "independent": Samples are denoised indpendently. "pseudo": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs.'
+          - names:
+              - --p-chimera-method
+            argument: TEXT Choices('consensus', 'none', 'pooled')
+            description: 'The method used to remove chimeras. "none": No chimera removal is performed. "pooled": All reads are pooled prior to chimera detection. "consensus": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: ''consensus'']'
+          - names:
+              - --p-min-fold-parent-over-abundance
+            argument: NUMBER
+            description: 'The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is "none". [default: 1.0]'
+          - names:
+              - --p-allow-one-off
+              - --p-no-allow-one-off
+            argument: ""
+            description: Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is TrueIf True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera.
+          - names:
+              - --p-n-threads
+            argument: NTHREADS
+            description: 'The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]'
+          - names:
+              - --p-n-reads-learn
+            argument: INTEGER
+            description: The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model.
+          - names:
+              - --p-hashed-feature-ids
+              - --p-no-hashed-feature-ids
+            argument: ""
+            description: 'If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]'
+          - names:
+              - --p-retain-all-samples
+              - --p-no-retain-all-samples
+            argument: ""
+            description: If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table.
+          - names:
+              - --o-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting feature table. [required]
+          - names:
+              - --o-representative-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence, and these sequences will be the joined paired-end sequences. [required]
+          - names:
+              - --o-denoising-stats
+            argument: ARTIFACT SampleData[DADA2Stats]
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: denoise-pyro
+        description: Denoise and dereplicate single-end pyrosequences
+        usage: qiime dada2 denoise-pyro [OPTIONS]
+        options:
+          - names:
+              - --i-demultiplexed-seqs
+            argument: ARTIFACT SampleData[SequencesWithQuality]
+            description: The single-end demultiplexed pyrosequencing sequences (e.g. 454, IonTorrent) to be denoised.
+          - names:
+              - --p-trunc-len
+            argument: INTEGER
+            description: Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed [required]
+          - names:
+              - --p-trim-left
+            argument: INTEGER
+            description: 'Position at which sequences should be trimmed due to low quality. This trims the 5'' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]'
+          - names:
+              - --p-max-ee
+            argument: NUMBER
+            description: 'Reads with number of expected errors higher than this value will be discarded. [default: 2.0]'
+          - names:
+              - --p-trunc-q
+            argument: INTEGER
+            description: 'Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]'
+          - names:
+              - --p-max-len
+            argument: INTEGER
+            description: 'Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length. [default: 0]'
+          - names:
+              - --p-pooling-method
+            argument: TEXT Choices('independent', 'pseudo')
+            description: 'The method used to pool samples for denoising. "independent": Samples are denoised independently. "pseudo": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs.'
+          - names:
+              - --p-chimera-method
+            argument: TEXT Choices('consensus', 'none', 'pooled')
+            description: 'The method used to remove chimeras. "none": No chimera removal is performed. "pooled": All reads are pooled prior to chimera detection. "consensus": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: ''consensus'']'
+          - names:
+              - --p-min-fold-parent-over-abundance
+            argument: NUMBER
+            description: 'The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is "none". [default: 1.0]'
+          - names:
+              - --p-allow-one-off
+              - --p-no-allow-one-off
+            argument: ""
+            description: 'Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is True. If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera. [default: False]'
+          - names:
+              - --p-n-threads
+            argument: NTHREADS
+            description: 'The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]'
+          - names:
+              - --p-n-reads-learn
+            argument: INTEGER
+            description: The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model.
+          - names:
+              - --p-hashed-feature-ids
+              - --p-no-hashed-feature-ids
+            argument: ""
+            description: 'If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]'
+          - names:
+              - --p-retain-all-samples
+              - --p-no-retain-all-samples
+            argument: ""
+            description: If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table.
+          - names:
+              - --o-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting feature table. [required]
+          - names:
+              - --o-representative-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]
+          - names:
+              - --o-denoising-stats
+            argument: ARTIFACT SampleData[DADA2Stats]
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: denoise-single
+        description: Denoise and dereplicate single-end sequences
+        usage: qiime dada2 denoise-single [OPTIONS]
+        options:
+          - names:
+              - --p-trunc-len
+            argument: INTEGER
+            description: Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed [required]
+          - names:
+              - --p-trim-left
+            argument: INTEGER
+            description: 'Position at which sequences should be trimmed due to low quality. This trims the 5'' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]'
+          - names:
+              - --p-max-ee
+            argument: NUMBER
+            description: 'Reads with number of expected errors higher than this value will be discarded. [default: 2.0]'
+          - names:
+              - --p-trunc-q
+            argument: INTEGER
+            description: 'Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]'
+          - names:
+              - --p-pooling-method
+            argument: TEXT Choices('independent', 'pseudo')
+            description: 'The method used to pool samples for denoising. "independent": Samples are denoised independently. "pseudo": The pseudo-pooling method is used to approximate pooling of samples. In short, samples are denoised independently once, ASVs detected in at least 2 samples are recorded, and samples are denoised independently a second time, but this time with prior knowledge of the recorded ASVs and thus higher sensitivity to those ASVs.'
+          - names:
+              - --p-chimera-method
+            argument: TEXT Choices('consensus', 'none', 'pooled')
+            description: 'The method used to remove chimeras. "none": No chimera removal is performed. "pooled": All reads are pooled prior to chimera detection. "consensus": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: ''consensus'']'
+          - names:
+              - --p-min-fold-parent-over-abundance
+            argument: NUMBER
+            description: 'The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is "none". [default: 1.0]'
+          - names:
+              - --p-allow-one-off
+              - --p-no-allow-one-off
+            argument: ""
+            description: 'Bimeras that are one-off from exact are also identified if the `allow-one-off` argument is True.If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera. [default: False]'
+          - names:
+              - --p-n-threads
+            argument: NTHREADS
+            description: 'The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used. [default: 1]'
+          - names:
+              - --p-n-reads-learn
+            argument: INTEGER
+            description: The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model.
+          - names:
+              - --p-hashed-feature-ids
+              - --p-no-hashed-feature-ids
+            argument: ""
+            description: 'If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: True]'
+          - names:
+              - --p-retain-all-samples
+              - --p-no-retain-all-samples
+            argument: ""
+            description: If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table.
+          - names:
+              - --o-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting feature table. [required]
+          - names:
+              - --o-representative-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. [required]
+          - names:
+              - --o-denoising-stats
+            argument: ARTIFACT SampleData[DADA2Stats]
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+  - name: deblur
+    description: Plugin for sequence quality control with Deblur.
+    usage: qiime deblur [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: denoise-16S
+        description: Deblur sequences using a 16S positive filter.
+        usage: qiime deblur denoise-16S [OPTIONS]
+        options:
+          - names:
+              - --p-trim-length
+            argument: INTEGER
+            description: Sequence trim length, specify -1 to disable trimming. [required]
+          - names:
+              - --p-sample-stats
+              - --p-no-sample-stats
+            argument: ""
+            description: 'If true, gather stats per sample. [default: False]'
+          - names:
+              - --p-mean-error
+            argument: NUMBER
+            description: 'The mean per nucleotide error, used for original sequence estimate. [default: 0.005]'
+          - names:
+              - --p-indel-prob
+            argument: NUMBER
+            description: 'Insertion/deletion (indel) probability (same for N indels). [default: 0.01]'
+          - names:
+              - --p-indel-max
+            argument: INTEGER
+            description: 'Maximum number of insertion/deletions. [default: 3]'
+          - names:
+              - --p-min-reads
+            argument: INTEGER
+            description: 'Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]'
+          - names:
+              - --p-min-size
+            argument: INTEGER
+            description: 'In each sample, discard all features with an abundance less than min-size. [default: 2]'
+          - names:
+              - --p-jobs-to-start
+            argument: NTHREADS
+            description: Number of jobs to start (if to run in parallel).
+          - names:
+              - --p-hashed-feature-ids
+              - --p-no-hashed-feature-ids
+            argument: ""
+            description: 'If true, hash the feature IDs. [default: True]'
+          - names:
+              - --p-left-trim-len
+            argument: INTEGER
+            description: Sequence trimming from the 5' end. A value of 0 will
+          - names:
+              - --o-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting denoised feature table. [required]
+          - names:
+              - --o-representative-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The resulting feature sequences. [required]
+          - names:
+              - --o-stats
+            argument: ARTIFACT
+            description: Per-sample stats if requested.
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: denoise-other
+        description: Deblur sequences using a user-specified positive filter.
+        usage: qiime deblur denoise-other [OPTIONS]
+        options:
+          - names:
+              - --i-demultiplexed-seqs
+            argument: ""
+            description: ARTIFACT SampleData[SequencesWithQuality |
+          - names:
+              - --i-reference-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Positive filtering database. Keep all sequences aligning to these sequences. [required]
+          - names:
+              - --p-trim-length
+            argument: INTEGER
+            description: Sequence trim length, specify -1 to disable trimming. [required]
+          - names:
+              - --p-sample-stats
+              - --p-no-sample-stats
+            argument: ""
+            description: 'If true, gather stats per sample. [default: False]'
+          - names:
+              - --p-mean-error
+            argument: NUMBER
+            description: 'The mean per nucleotide error, used for original sequence estimate. [default: 0.005]'
+          - names:
+              - --p-indel-prob
+            argument: NUMBER
+            description: 'Insertion/deletion (indel) probability (same for N indels). [default: 0.01]'
+          - names:
+              - --p-indel-max
+            argument: INTEGER
+            description: 'Maximum number of insertion/deletions. [default: 3]'
+          - names:
+              - --p-min-reads
+            argument: INTEGER
+            description: 'Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]'
+          - names:
+              - --p-min-size
+            argument: INTEGER
+            description: 'In each sample, discard all features with an abundance less than min-size. [default: 2]'
+          - names:
+              - --p-jobs-to-start
+            argument: NTHREADS
+            description: Number of jobs to start (if to run in parallel).
+          - names:
+              - --p-hashed-feature-ids
+              - --p-no-hashed-feature-ids
+            argument: ""
+            description: 'If true, hash the feature IDs. [default: True]'
+          - names:
+              - --p-left-trim-len
+            argument: INTEGER
+            description: Sequence trimming from the 5' end. A value of 0 will
+          - names:
+              - --o-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting denoised feature table. [required]
+          - names:
+              - --o-representative-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The resulting feature sequences. [required]
+          - names:
+              - --o-stats
+            argument: ARTIFACT
+            description: Per-sample stats if requested. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: visualize-stats
+        description: Visualize Deblur stats per sample.
+        usage: qiime deblur visualize-stats [OPTIONS]
+        options:
+          - names:
+              - --i-deblur-stats
+            argument: ARTIFACT
+            description: DeblurStats Summary statistics of the Deblur process. [required]
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+  - name: demux
+    description: Plugin for demultiplexing & viewing sequence quality.
+    usage: qiime demux [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: emp-paired
+        description: Demultiplex paired-end sequence data generated with the EMP protocol.
+        usage: qiime demux emp-paired [OPTIONS]
+        options:
+          - names:
+              - --i-seqs
+            argument: ARTIFACT EMPPairedEndSequences
+            description: The paired-end sequences to be demultiplexed.
+          - names:
+              - --m-barcodes-file
+              - --m-barcodes-column
+            argument: METADATA
+            description: The sample metadata column containing the per-sample barcodes. [required]
+          - names:
+              - --p-golay-error-correction
+              - --p-no-golay-error-correction
+            argument: ""
+            description: 'Perform 12nt Golay error correction on the barcode reads. [default: True]'
+          - names:
+              - --p-rev-comp-barcodes
+              - --p-no-rev-comp-barcodes
+            argument: ""
+            description: If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing.
+          - names:
+              - --p-rev-comp-mapping-barcodes
+              - --p-no-rev-comp-mapping-barcodes
+            argument: ""
+            description: 'If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]'
+          - names:
+              - --p-ignore-description-mismatch
+              - --p-no-ignore-description-mismatch
+            argument: ""
+            description: 'If enabled, ignore mismatches in sequence record description fields. [default: False]'
+          - names:
+              - --o-error-correction-details
+            argument: ARTIFACT ErrorCorrectionDetails
+            description: Detail about the barcode error corrections. [required]
+          - names:
+              - --o-per-sample-sequences
+            argument: ARTIFACT
+            description: SampleData[PairedEndSequencesWithQuality]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: emp-single
+        description: Demultiplex sequence data generated with the EMP protocol.
+        usage: qiime demux emp-single [OPTIONS]
+        options:
+          - names:
+              - --m-barcodes-file
+              - --m-barcodes-column
+            argument: METADATA
+            description: The sample metadata column containing the per-sample barcodes. [required]
+          - names:
+              - --p-golay-error-correction
+              - --p-no-golay-error-correction
+            argument: ""
+            description: 'Perform 12nt Golay error correction on the barcode reads. [default: True]'
+          - names:
+              - --p-rev-comp-barcodes
+              - --p-no-rev-comp-barcodes
+            argument: ""
+            description: If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing.
+          - names:
+              - --p-rev-comp-mapping-barcodes
+              - --p-no-rev-comp-mapping-barcodes
+            argument: ""
+            description: 'If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]'
+          - names:
+              - --p-ignore-description-mismatch
+              - --p-no-ignore-description-mismatch
+            argument: ""
+            description: 'If enabled, ignore mismatches in sequence record description fields. [default: False]'
+          - names:
+              - --o-per-sample-sequences
+            argument: ARTIFACT SampleData[SequencesWithQuality]
+            description: The resulting demultiplexed sequences. [required]
+          - names:
+              - --o-error-correction-details
+            argument: ARTIFACT ErrorCorrectionDetails
+            description: Detail about the barcode error corrections. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: filter-samples
+        description: Filter samples out of demultiplexed data.
+        usage: qiime demux filter-samples [OPTIONS]
+        options:
+          - names:
+            - --i-demux
+            argument: ARTIFACT
+            description: The demultiplexed data from which samples should be filtered. [required]
+          - names:
+            - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata indicating which sample ids to filter. [required]
+          - names:
+              - --p-where
+            argument: TEXT
+            description: Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]
+          - names:
+              - --p-exclude-ids
+              - --p-no-exclude-ids
+            argument: ""
+            description: 'Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: partition-samples-paired
+        description: Split demultiplexed sequence data into partitions.
+        usage: qiime demux partition-samples-paired [OPTIONS]
+        options:
+          - names:
+              - --i-demux
+            argument: ARTIFACT SampleData[PairedEndSequencesWithQuality]
+            description: The demultiplexed sequences to partition. [required]
+          - names:
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the demultiplexed
+          - names:
+              - --o-partitioned-demux
+            argument: ARTIFACTS...
+            description: Collection[SampleData[PairedEndSequencesWithQuality]]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: partition-samples-single
+        description: Split demultiplexed sequence data into partitions.
+        usage: qiime demux partition-samples-single [OPTIONS]
+        options:
+          - names:
+              - --i-demux
+            argument: ARTIFACT SampleData[SequencesWithQuality]
+            description: The demultiplexed sequences to partition. [required]
+          - names:
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the demultiplexed
+          - names:
+              - --o-partitioned-demux
+            argument: ARTIFACTS...
+            description: Collection[SampleData[SequencesWithQuality]]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: subsample-paired
+        description: Subsample paired-end sequences without replacement.
+        usage: qiime demux subsample-paired [OPTIONS]
+        options:
+          - names:
+              - --i-sequences
+            argument: ARTIFACT SampleData[PairedEndSequencesWithQuality]
+            description: The demultiplexed sequences to be subsampled.
+          - names:
+              - --p-fraction
+            argument: PROPORTION Range(0, 1, inclusive_start=False)
+            description: The fraction of sequences to retain in subsample.
+          - names:
+              - --o-subsampled-sequences
+            argument: ARTIFACT
+            description: SampleData[PairedEndSequencesWithQuality]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: subsample-single
+        description: Subsample single-end sequences without replacement.
+        usage: qiime demux subsample-single [OPTIONS]
+        options:
+          - names:
+              - --p-fraction
+            argument: PROPORTION Range(0, 1, inclusive_start=False)
+            description: The fraction of sequences to retain in subsample.
+          - names:
+              - --o-subsampled-sequences
+            argument: ARTIFACT SampleData[SequencesWithQuality]
+            description: The subsampled sequences. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: summarize
+        description: Summarize counts per sample.
+        usage: qiime demux summarize [OPTIONS]
+        options:
+          - names:
+              - --p-n
+            argument: INTEGER
+            description: The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences.
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: tabulate-read-counts
+        description: Tabulate counts per sample
+        usage: qiime demux tabulate-read-counts [OPTIONS]
+        options:
+          - names:
+              - --o-counts
+            argument: ARTIFACT
+            description: ImmutableMetadata [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+  - name: diversity
+    description: Plugin for exploring community diversity.
+    usage: qiime diversity [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: adonis
+        description: adonis PERMANOVA test for beta group significance
+        usage: qiime diversity adonis [OPTIONS]
+        options:
+          - names:
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of distances between pairs of samples. [required]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata containing formula terms. [required]
+          - names:
+              - --p-formula
+            argument: TEXT
+            description: Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula "treatment+block" would test whether the input distance matrix partitions based on "treatment" and "block" sample metadata. The formula "treatment*block" would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]
+          - names:
+              - --p-n-jobs
+            argument: NTHREADS
+            description: Number of parallel processes to run
+          - names:
+              - --p-permutations
+            argument: INTEGER
+            description: The number of permutations to be run when computing
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: alpha
+        description: Alpha diversity
+        usage: qiime diversity alpha [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable
+            description: The feature table containing the samples for which
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence
+            description: The feature table containing the samples for which
+          - names:
+              - --o-alpha-diversity
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector containing per-sample alpha diversities.
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: alpha-correlation
+        description: Alpha diversity correlation
+        usage: qiime diversity alpha-correlation [OPTIONS]
+        options:
+          - names:
+              - --i-alpha-diversity
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector of alpha diversity values by sample. [required]
+          - names:
+              - --p-method
+            argument: TEXT Choices('spearman', 'pearson')
+            description: The correlation test to be applied.
+          - names:
+              - --p-intersect-ids
+              - --p-no-intersect-ids
+            argument: ""
+            description: 'If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs. [default: False]'
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata.
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: alpha-group-significance
+        description: Alpha diversity comparisons
+        usage: qiime diversity alpha-group-significance [OPTIONS]
+        options:
+          - names:
+              - --i-alpha-diversity
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector of alpha diversity values by sample. [required]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata. [required]
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: alpha-phylogenetic
+        description: Alpha diversity (phylogenetic)
+        usage: qiime diversity alpha-phylogenetic [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
+            description: The feature table containing the samples for which alpha diversity should be computed. [required]
+          - names:
+              - --i-phylogeny
+            argument: ARTIFACT
+            description: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. [required]
+          - names:
+              - --p-metric
+            argument: TEXT
+            description: The alpha diversity metric to be computed. [required]
+          - names:
+              - --o-alpha-diversity
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector containing per-sample alpha diversities. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: alpha-rarefaction
+        description: Alpha rarefaction curves
+        usage: qiime diversity alpha-rarefaction [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Feature table to compute rarefaction curves from. [required]
+          - names:
+              - --i-phylogeny
+            argument: ARTIFACT
+            description: Optional phylogeny for phylogenetic metrics.
+          - names:
+              - --p-max-depth
+            argument: INTEGER
+            description: The maximum rarefaction depth. Must be greater than min-depth. [required]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata.
+          - names:
+              - --p-min-depth
+            argument: INTEGER
+            description: The minimum rarefaction depth.
+          - names:
+              - --p-steps
+            argument: INTEGER
+            description: 'The number of rarefaction depths to include between min-depth and max-depth. [default: 10]'
+          - names:
+              - --p-iterations
+            argument: INTEGER
+            description: 'The number of rarefied feature tables to compute at each step. [default: 10]'
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: beta
+        description: Beta diversity
+        usage: qiime diversity beta [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: 'ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]'
+            description: The feature table containing the samples over which beta diversity should be computed. [required]
+          - names:
+              - --p-metric
+            argument: '{aitchison, braycurtis, canberra, canberra_adkins, chebyshev, cityblock, correlation, cosine, dice, euclidean, hamming, jaccard, jensenshannon, kulsinski, matching, minkowski, rogerstanimoto, russellrao, seuclidean, sokalmichener, sokalsneath, sqeuclidean, yule}'
+            description: The beta diversity metric to be computed.
+          - names:
+              - --p-pseudocount
+            argument: INTEGER
+            description: A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics.
+          - names:
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = ''auto'', one job will be launched for each identified CPU core on the host. [default: 1]'
+          - names:
+              - --o-distance-matrix
+            argument: ARTIFACT
+            description: DistanceMatrix The resulting distance matrix. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: beta-correlation
+        description: Beta diversity correlation
+        usage: qiime diversity beta-correlation [OPTIONS]
+        options:
+          - names:
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of distances between pairs of samples. [required]
+          - names:
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Numeric metadata column from which to compute pairwise Euclidean distances [required]
+          - names:
+              - --p-method
+            argument: TEXT Choices('spearman', 'pearson')
+            description: 'The correlation test to be applied in the Mantel test. [default: ''spearman'']'
+          - names:
+              - --p-permutations
+            argument: INTEGER
+            description: 'The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]'
+          - names:
+              - --p-intersect-ids
+              - --p-no-intersect-ids
+            argument: ""
+            description: 'If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]'
+          - names:
+              - --p-label1
+            argument: TEXT
+            description: 'Label for `distance-matrix` in the output visualization. [default: ''Distance Matrix'']'
+          - names:
+              - --p-label2
+            argument: TEXT
+            description: 'Label for `metadata-distance-matrix` in the output visualization. [default: ''Metadata'']'
+          - names:
+              - --p-permutations
+            argument: INTEGER
+            description: The number of permutations to be run when computing p-values.
+          - names:
+              - --o-metadata-distance-matrix
+            argument: ARTIFACT
+            description: 'The Distance Matrix produced from the metadata column and used in the mantel test [required]'
+          - names:
+              - --o-mantel-scatter-visualization
+            argument: VISUALIZATION
+            description: 'Scatter plot rendering of the manteltest results [required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: beta-group-significance
+        description: Beta diversity group significance
+        usage: qiime diversity beta-group-significance [OPTIONS]
+        options:
+          - names:
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of distances between pairs of samples.
+          - names:
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Categorical sample metadata column. [required]
+          - names:
+              - --p-method
+            argument: TEXT Choices('permanova', 'anosim', 'permdisp')
+            description: The group significance test to be applied.
+          - names:
+              - --p-pairwise
+              - --p-no-pairwise
+            argument: ""
+            description: 'Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column. [default: False]'
+          - names:
+              - --p-permutations
+            argument: INTEGER
+            description: 'The number of permutations to be run when computing p-values. [default: 999]'
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: beta-phylogenetic
+        description: Beta diversity (phylogenetic)
+        usage: qiime diversity beta-phylogenetic [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: 'ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]'
+            description: The feature table containing the samples over which beta diversity should be computed. [required]
+          - names:
+              - --i-phylogeny
+            argument: ARTIFACT
+            description: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]
+          - names:
+              - --p-metric
+            argument: '{generalized_unifrac, unweighted_unifrac, weighted_normalized_unifrac, weighted_unifrac}'
+            description: The beta diversity metric to be computed. [required]
+          - names:
+              - --p-threads
+            argument: NTHREADS
+            description: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.
+          - names:
+              - --p-variance-adjusted
+              - --p-no-variance-adjusted
+            argument: ""
+            description: 'Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]'
+          - names:
+              - --p-alpha
+            argument: PROPORTION Range(0, 1, inclusive_end=True)
+            description: This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized. [optional]
+          - names:
+              - --p-bypass-tips
+              - --p-no-bypass-tips
+            argument: ""
+            description: 'In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]'
+          - names:
+              - --o-distance-matrix
+            argument: ARTIFACT
+            description: The resulting distance matrix. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: beta-rarefaction
+        description: Beta diversity rarefaction
+        usage: qiime diversity beta-rarefaction [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Feature table upon which to perform beta diversity rarefaction analyses. [required]
+          - names:
+              - --i-phylogeny
+            argument: ARTIFACT
+            description: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required for phylogenetic metrics] [optional]
+          - names:
+              - --p-metric
+            argument: '{aitchison, braycurtis, canberra, canberra_adkins, chebyshev, cityblock, correlation, cosine, dice, euclidean, generalized_unifrac, hamming, jaccard, jensenshannon, kulsinski, matching, minkowski, rogerstanimoto, russellrao, seuclidean, sokalmichener, sokalsneath, sqeuclidean, unweighted_unifrac, weighted_normalized_unifrac, weighted_unifrac, yule}'
+            description: The beta diversity metric to be computed. [required]
+          - names:
+              - --p-clustering-method
+            argument: '{nj, upgma}'
+            description: Samples can be clustered with neighbor joining or UPGMA. An arbitrary rarefaction trial will be used for the tree, and the remaining trials are used to calculate the support of the internal nodes of that tree. [required]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata used for the Emperor jackknifed PCoA plot. [required]
+          - names:
+              - --p-sampling-depth
+            argument: INTEGER
+            description: The total frequency that each sample should be rarefied to prior to computing the diversity metric. [required]
+          - names:
+              - --p-iterations
+            argument: INTEGER
+            description: 'Number of times to rarefy the feature table at a given sampling depth. [default: 10]'
+          - names:
+              - --p-clustering-method
+            argument: TEXT Choices('nj', 'upgma')
+            description: Samples can be clustered with neighbor joining or UPGMA. An arbitrary rarefaction trial will be used for the tree, and the remaining trials are used to calculate the support of the internal nodes of that tree. [required]
+          - names:
+              - --p-correlation-method
+            argument: TEXT Choices('pearson', 'spearman')
+            description: 'The Mantel correlation test to be applied when computing correlation between beta diversity distance matrices. [default: ''spearman'']'
+          - names:
+              - --p-color-scheme
+            argument: '{BrBG, BrBG_r, PRGn, PRGn_r, PiYG, PiYG_r, PuOr, PuOr_r, RdBu, RdBu_r, RdGy, RdGy_r, RdYlBu, RdYlBu_r, RdYlGn, RdYlGn_r}'
+            description: The matplotlib color scheme to generate the heatmap with.
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: bioenv
+        description: bioenv
+        usage: qiime diversity bioenv [OPTIONS]
+        options:
+          - names:
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of distances between pairs of samples.
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata.
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: core-metrics
+        description: Core diversity metrics (non-phylogenetic)
+        usage: qiime diversity core-metrics [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table containing the samples over which diversity metrics should be computed. [required]
+          - names:
+              - --p-sampling-depth
+            argument: INTEGER
+            description: The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata to use in the emperor plots. [required]
+          - names:
+              - --p-with-replacement
+              - --p-no-with-replacement
+            argument: ""
+            description: 'Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]'
+          - names:
+              - --p-n-jobs
+            argument: NTHREADS
+            description: '[beta methods only] - The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = ''auto'', one job will be launched for each identified CPU core on the host. [default: 1]'
+          - names:
+              - --p-ignore-missing-samples
+              - --p-no-ignore-missing-samples
+            argument: ""
+            description: 'If set to `True` samples and features without metadata are included by setting all metadata values to: "This element has no metadata". By default an exception will be raised if missing elements are encountered. Note, this flag only takes effect if there is at least one overlapping element.'
+          - names:
+              - --o-rarefied-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting rarefied feature table. [required]
+          - names:
+              - --o-observed-features-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector of Observed Features values by sample. [required]
+          - names:
+              - --o-shannon-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector of Shannon diversity values by sample. [required]
+          - names:
+              - --o-evenness-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector of Pielou's evenness values by sample. [required]
+          - names:
+              - --o-jaccard-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of Jaccard distances between pairs of samples. [required]
+          - names:
+              - --o-bray-curtis-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of Bray-Curtis distances between pairs of samples. [required]
+          - names:
+              - --o-jaccard-pcoa-results
+            argument: ARTIFACT
+            description: PCoA matrix computed from Jaccard distances between samples. [required]
+          - names:
+              - --o-bray-curtis-pcoa-results
+            argument: ARTIFACT
+            description: PCoA matrix computed from Bray-Curtis distances Bray-Curtis. [required]
+          - names:
+              - --o-jaccard-emperor
+            argument: VISUALIZATION
+            description: Emperor plot of the PCoA matrix computed from Jaccard. [required]
+          - names:
+              - --o-bray-curtis-emperor
+            argument: VISUALIZATION
+            description: Emperor plot of the PCoA matrix computed from Bray-Curtis. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: core-metrics-phylogenetic
+        description: Core diversity metrics (phylogenetic and non-phylogenetic)
+        usage: qiime diversity core-metrics-phylogenetic [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table containing the samples over which diversity metrics should be computed. [required]
+          - names:
+              - --i-phylogeny
+            argument: ARTIFACT
+            description: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]
+          - names:
+              - --p-sampling-depth
+            argument: INTEGER
+            description: The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata to use in the emperor plots. [required]
+          - names:
+              - --p-with-replacement
+              - --p-no-with-replacement
+            argument: ""
+            description: 'Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]'
+          - names:
+              - --o-rarefied-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting rarefied feature table. [required]
+          - names:
+              - --o-faith-pd-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector of Faith PD values by sample. [required]
+          - names:
+              - --o-observed-features-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector of Observed Features values by sample. [required]
+          - names:
+              - --o-shannon-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector of Shannon diversity values by sample. [required]
+          - names:
+              - --o-evenness-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector of Pielou's evenness values by sample. [required]
+          - names:
+              - --o-unweighted-unifrac-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of unweighted UniFrac distances between pairs of samples. [required]
+          - names:
+              - --o-weighted-unifrac-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of weighted UniFrac distances between pairs of samples. [required]
+          - names:
+              - --o-jaccard-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of Jaccard distances between pairs of samples. [required]
+          - names:
+              - --o-bray-curtis-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of Bray-Curtis distances between pairs of samples. [required]
+          - names:
+              - --o-unweighted-unifrac-pcoa-results
+            argument: ARTIFACT
+            description: PCoA matrix computed from unweighted UniFrac distances between samples. [required]
+          - names:
+              - --o-weighted-unifrac-pcoa-results
+            argument: ARTIFACT
+            description: PCoA matrix computed from weighted UniFrac distances between samples. [required]
+          - names:
+              - --o-jaccard-pcoa-results
+            argument: ARTIFACT
+            description: PCoA matrix computed from Jaccard distances between samples. [required]
+          - names:
+              - --o-bray-curtis-pcoa-results
+            argument: ARTIFACT
+            description: PCoA matrix computed from Bray-Curtis distances samples. [required]
+          - names:
+              - --o-unweighted-unifrac-emperor
+            argument: VISUALIZATION
+            description: Emperor plot of the PCoA matrix computed from unweighted UniFrac. [required]
+          - names:
+              - --o-weighted-unifrac-emperor
+            argument: VISUALIZATION
+            description: Emperor plot of the PCoA matrix computed from weighted UniFrac. [required]
+          - names:
+              - --o-jaccard-emperor
+            argument: VISUALIZATION
+            description: Emperor plot of the PCoA matrix computed from Jaccard. [required]
+          - names:
+              - --o-bray-curtis-emperor
+            argument: VISUALIZATION
+            description: Emperor plot of the PCoA matrix computed from Bray-Curtis. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: filter-alpha-diversity
+        description: Filter samples from an alpha diversity metric.
+        usage: qiime diversity filter-alpha-diversity [OPTIONS]
+        options:
+          - names:
+              - --i-alpha-diversity
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Alpha diversity sample data to filter by sample. [required]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata used to select samples to retain from the sample data (default) or select samples to exclude using the `exclude-ids` parameter. [required]
+          - names:
+              - --p-where
+            argument: TEXT
+            description: SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered alpha diversity artifact. If not provided, all samples in `metadata` that are also in the input alpha diversity artifact will be retained. [optional]
+          - names:
+              - --p-exclude-ids
+              - --p-no-exclude-ids
+            argument: ""
+            description: If `True`, the samples selected by `metadata` or the `where` parameters will be excluded from the filtered alpha diversity artifact instead of being retained.
+          - names:
+              - --o-filtered-alpha-diversity
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: filter-distance-matrix
+        description: Filter samples from a distance matrix.
+        usage: qiime diversity filter-distance-matrix [OPTIONS]
+        options:
+          - names:
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: Distance matrix to filter by sample. [required]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude-ids` when selecting samples to discard. [required]
+          - names:
+              - --p-where
+            argument: TEXT
+            description: SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained. [optional]
+          - names:
+              - --p-exclude-ids
+              - --p-no-exclude-ids
+            argument: ""
+            description: If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained.
+          - names:
+              - --o-filtered-distance-matrix
+            argument: ARTIFACT
+            description: Distance matrix filtered to include samples matching
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: mantel
+        description: Apply the Mantel test to two distance matrices
+        usage: qiime diversity mantel [OPTIONS]
+        options:
+          - names:
+              - --i-dm1
+            argument: ARTIFACT
+            description: Matrix of distances between pairs of samples. [required]
+          - names:
+              - --i-dm2
+            argument: ARTIFACT
+            description: Matrix of distances between pairs of samples. [required]
+          - names:
+              - --p-method
+            argument: '{spearman, pearson}'
+            description: The correlation test to be applied in the Mantel test.
+          - names:
+              - --p-permutations
+            argument: INTEGER
+            description: The number of permutations to be run when computing p-values.
+          - names:
+              - --p-intersect-ids
+              - --p-no-intersect-ids
+            argument: ""
+            description: 'If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]'
+          - names:
+              - --p-label1
+            argument: TEXT
+            description: Label for `dm1` in the output visualization.
+          - names:
+              - --p-label2
+            argument: TEXT
+            description: Label for `dm2` in the output visualization.
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: partial-procrustes
+        description: Partial Procrustes
+        usage: qiime diversity partial-procrustes [OPTIONS]
+        options:
+          - names:
+              - --i-reference
+            argument: ARTIFACT
+            description: The ordination matrix to which data is fitted to. [required]
+          - names:
+              - --i-other
+            argument: ARTIFACT
+            description: The ordination matrix that's fitted to the reference ordination. [required]
+          - names:
+              - --m-pairing-file
+            argument: METADATA
+            description: The metadata file.
+          - names:
+              - --m-pairing-column
+            argument: COLUMN
+            description: The metadata column describing sample pairs which exist. [required]
+          - names:
+              - --p-dimensions
+            argument: INTEGER
+            description: The number of dimensions to use when fitting the two matrices of the reference ordination. [required]
+          - names:
+              - --o-transformed
+            argument: ARTIFACT
+            description: The 'other' ordination transformed into the space of the reference ordination. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: pcoa
+        description: Principal Coordinate Analysis
+        usage: qiime diversity pcoa [OPTIONS]
+        options:
+          - names:
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: The distance matrix on which PCoA should be computed. [required]
+          - names:
+              - --p-number-of-dimensions
+            argument: INTEGER
+            description: Dimensions to reduce the distance matrix to. This number determines how many eigenvectors and eigenvalues are returned,and influences the choice of algorithm used to compute them. By default, uses the default eigendecomposition method, SciPy's eigh, which computes all eigenvectors and eigenvalues in an exact manner. For very large matrices, this is expected to be slow. If a value is specified for this parameter, then the fast, heuristic eigendecomposition algorithm fsvd is used, which only computes and returns the number of dimensions specified, but suffers some degree of accuracy loss, the magnitude of which varies across different datasets. [optional]
+          - names:
+              - --o-pcoa
+            argument: ARTIFACT
+            description: The resulting PCoA matrix.
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: pcoa-biplot
+        description: Principal Coordinate Analysis Biplot
+        usage: qiime diversity pcoa-biplot [OPTIONS]
+        options:
+          - names:
+              - --i-pcoa
+            argument: ARTIFACT
+            description: The PCoA where the features will be projected onto.
+          - names:
+              - --i-features
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: Variables to project onto the PCoA matrix [required]
+          - names:
+              - --o-biplot
+            argument: ARTIFACT
+            description: The resulting PCoA matrix. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: procrustes-analysis
+        description: Procrustes Analysis
+        usage: qiime diversity procrustes-analysis [OPTIONS]
+        options:
+          - names:
+              - --i-reference
+            argument: ARTIFACT
+            description: The ordination matrix to which data is fitted to. [required]
+          - names:
+              - --i-other
+            argument: ARTIFACT
+            description: The ordination matrix that's fitted to the reference ordination. [required]
+          - names:
+              - --p-dimensions
+            argument: INTEGER
+            description: 'The number of dimensions to use when fitting the two matrices [default: 5]'
+          - names:
+              - --p-permutations
+            argument: VALUE
+            description: 'The number of permutations to be run when computing p-values. Supplying a value of `disable` will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]'
+          - names:
+              - --o-transformed-reference
+            argument: ARTIFACT
+            description: A normalized version of the "reference" ordination matrix. [required]
+          - names:
+              - --o-transformed-other
+            argument: ARTIFACT
+            description: A normalized and fitted version of the "other" ordination matrix. [required]
+          - names:
+              - --o-disparity-results
+            argument: ARTIFACT
+            description: The sum of the squares of the pointwise differences between the two input datasets & its p value. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: tsne
+        description: t-distributed stochastic neighbor embedding
+        usage: qiime diversity tsne [OPTIONS]
+        options:
+          - names:
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: The distance matrix on which t-SNE should be computed. [required]
+          - names:
+              - --p-number-of-dimensions
+            argument: INTEGER
+            description: Dimensions to reduce the distance matrix to. [required]
+          - names:
+              - --p-perplexity
+            argument: NUMBER
+            description: 'Provide the balance between local and global structure. Low values concentrate on local structure. [default: 25.0]'
+          - names:
+              - --p-n-iter
+            argument: INTEGER
+            description: '[default: 1000]'
+          - names:
+              - --p-learning-rate
+            argument: NUMBER
+            description: 'Controls how much the weights are adjusted at each update. [default: 200.0]'
+          - names:
+              - --p-early-exaggeration
+            argument: NUMBER
+            description: 'Affects the tightness of the shown clusters. Larger values increase the distance between natural clusters in the embedded space. [default: 12.0]'
+          - names:
+              - --p-random-state
+            argument: INTEGER
+            description: Seed used by random number generator. [optional]
+          - names:
+              - --o-tsne
+            argument: ARTIFACT
+            description: The resulting t-SNE matrix. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: umap
+        description: Uniform Manifold Approximation and Projection
+        usage: qiime diversity umap [OPTIONS]
+        options:
+          - names:
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: The distance matrix on which UMAP should be computed. [required]
+          - names:
+              - --p-number-of-dimensions
+            argument: INTEGER
+            description: Dimensions to reduce the distance matrix to.
+          - names:
+              - --p-n-neighbors
+            argument: INTEGER
+            description: Provide the balance between local and global structure.
+          - names:
+              - --p-min-dist
+            argument: NUMBER
+            description: Controls the cluster size. Low values cause clumpier clusters.
+          - names:
+              - --p-random-state
+            argument: INTEGER
+            description: Seed used by random number generator. [optional]
+          - names:
+              - --o-umap
+            argument: ARTIFACT
+            description: The resulting UMAP matrix. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+  - name: diversity-lib
+    description: Plugin for computing community diversity.
+    usage: qiime diversity-lib [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: alpha-passthrough
+        description: Alpha Passthrough (non-phylogenetic)
+        usage: qiime diversity-lib alpha-passthrough [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table containing the samples for which a selected metric should be computed. [required]
+          - names:
+              - --p-metric
+            argument: TEXT
+            description: The alpha diversity metric to be computed. [required]
+          - names:
+              - --o-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector containing per-sample values for the chosen metric. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: beta-passthrough
+        description: Beta Passthrough (non-phylogenetic)
+        usage: qiime diversity-lib beta-passthrough [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table containing the samples over which beta diversity should be computed. [required]
+          - names:
+              - --p-metric
+            argument: TEXT
+            description: The beta diversity metric to be computed. [required]
+          - names:
+              - --p-pseudocount
+            argument: INTEGER
+            description: A pseudocount to handle zeros for compositional metrics.
+          - names:
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = ''auto'', one job will be launched for each identified CPU core on the host. [default: 1]'
+          - names:
+              - --o-distance-matrix
+            argument: ARTIFACT
+            description: DistanceMatrix The resulting distance matrix. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: beta-phylogenetic-passthrough
+        description: Beta Phylogenetic Passthrough
+        usage: qiime diversity-lib beta-phylogenetic-passthrough [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table containing the samples over which beta diversity should be computed. [required]
+          - names:
+              - --i-phylogeny
+            argument: ARTIFACT
+            description: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. [required]
+          - names:
+              - --p-metric
+            argument: TEXT
+            description: The beta diversity metric to be computed. [required]
+          - names:
+              - --p-threads
+            argument: NTHREADS
+            description: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.
+          - names:
+              - --p-variance-adjusted
+              - --p-no-variance-adjusted
+            argument: ""
+            description: 'Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]'
+          - names:
+              - --p-alpha
+            argument: PROPORTION Range(0, 1, inclusive_end=True)
+            description: This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized. [optional]
+          - names:
+              - --p-bypass-tips
+              - --p-no-bypass-tips
+            argument: ""
+            description: 'In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]'
+          - names:
+              - --o-distance-matrix
+            argument: ARTIFACT
+            description: DistanceMatrix The resulting distance matrix. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: bray-curtis
+        description: Bray-Curtis Dissimilarity
+        usage: qiime diversity-lib bray-curtis [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency]
+            description: The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.
+          - names:
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = ''auto'', one job will be launched for each identified CPU core on the host. [default: 1]'
+          - names:
+              - --o-distance-matrix
+            argument: ARTIFACT
+            description: Distance matrix for Bray-Curtis dissimilarity
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+          - names:
+              - --o-distance-matrix
+            argument: bray-curtis-dm.qza
+            description: '# ### example: use ''auto'' to run on all of host system''s available CPU cores'
+      - name: faith-pd
+        description: Faith's Phylogenetic Diversity
+        usage: qiime diversity-lib faith-pd [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable
+            description: The feature table containing the samples for which
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence
+            description: The feature table containing the samples for which
+          - names:
+              - --i-phylogeny
+            argument: ARTIFACT
+            description: Phylogenetic tree containing tip identifiers that   Phylogeny[Rooted] correspond to the feature identifiers in the table.
+          - names:
+              - --p-threads
+            argument: NTHREADS
+            description: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.
+          - names:
+              - --o-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector containing per-sample values for Faith's Phylogenetic Diversity. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: jaccard
+        description: Jaccard Distance
+        usage: qiime diversity-lib jaccard [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable
+            description: The feature table containing the samples for which
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence
+            description: The feature table containing the samples for which
+          - names:
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = ''auto'', one job will be launched for each identified CPU core on the host. [default: 1]'
+          - names:
+              - --o-distance-matrix
+            argument: ARTIFACT
+            description: Distance matrix for Jaccard index [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+          - names:
+              - --o-distance-matrix
+            argument: jaccard-dm.qza
+            description: '# ### example: use ''auto'' to run on all of host system''s available CPU cores'
+      - name: observed-features
+        description: Observed Features
+        usage: qiime diversity-lib observed-features [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable
+            description: The feature table containing the samples for which the
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence
+            description: The feature table containing the samples for which the
+          - names:
+              - --o-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector containing per-sample counts of observed features. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: pielou-evenness
+        description: Pielou's Evenness
+        usage: qiime diversity-lib pielou-evenness [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency]
+            description: The feature table containing the samples for which Pielou's evenness should be computed. [required]
+          - names:
+              - --p-drop-undefined-samples
+              - --p-no-drop-undefined-samples
+            argument: ""
+            description: 'Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector. [default: False]'
+          - names:
+              - --o-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector containing per-sample values for Pielou's Evenness. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: shannon-entropy
+        description: Shannon's Entropy
+        usage: qiime diversity-lib shannon-entropy [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency]
+            description: The feature table containing the samples for which Shannon's Entropy should be computed. [required]
+          - names:
+              - --p-drop-undefined-samples
+              - --p-no-drop-undefined-samples
+            argument: ""
+            description: 'Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector. [default: False]'
+          - names:
+              - --o-vector
+            argument: ARTIFACT SampleData[AlphaDiversity]
+            description: Vector containing per-sample values for Shannon's Entropy. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: unweighted-unifrac
+        description: Unweighted Unifrac
+        usage: qiime diversity-lib unweighted-unifrac [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable
+            description: The feature table containing the samples for which
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence
+            description: The feature table containing the samples for which
+          - names:
+              - --i-phylogeny
+            argument: ARTIFACT
+            description: Phylogenetic tree containing tip identifiers that   Phylogeny[Rooted] correspond to the feature identifiers in the table.
+          - names:
+              - --p-threads
+            argument: NTHREADS
+            description: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.
+          - names:
+              - --p-bypass-tips
+              - --p-no-bypass-tips
+            argument: ""
+            description: 'In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]'
+          - names:
+              - --o-distance-matrix
+            argument: ARTIFACT
+            description: Distance matrix for Unweighted Unifrac. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+          - names:
+              - --o-distance-matrix
+            argument: unweighted-unifrac-dm.qza
+            description: '# ### example: to run on n cores, replace 1 here with your preferred integer'
+      - name: weighted-unifrac
+        description: Weighted Unifrac
+        usage: qiime diversity-lib weighted-unifrac [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency]
+            description: The feature table containing the samples for which Weighted Unifrac should be computed. [required]
+          - names:
+              - --i-phylogeny
+            argument: ARTIFACT
+            description: Phylogenetic tree containing tip identifiers that
+          - names:
+              - --p-threads
+            argument: NTHREADS
+            description: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.
+          - names:
+              - --p-bypass-tips
+              - --p-no-bypass-tips
+            argument: ""
+            description: 'In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]'
+          - names:
+              - --o-distance-matrix
+            argument: ARTIFACT
+            description: Distance matrix for Unweighted Unifrac. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+          - names:
+              - --o-distance-matrix
+            argument: weighted-unifrac-dm.qza
+            description: '# ### example: to run on n cores, replace 1 here with your preferred integer'
+  - name: emperor
+    description: Plugin for ordination plotting with Emperor.
+    usage: qiime emperor [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: biplot
+        description: Visualize and Interact with Principal Coordinates Analysis
+        usage: qiime emperor biplot [OPTIONS]
+        options:
+          - names:
+              - --i-biplot
+            argument: ARTIFACT
+            description: The principal coordinates matrix to be plotted. [required]
+          - names:
+              - --m-sample-metadata-file
+            argument: METADATA...
+            description: The sample metadata [required]
+          - names:
+              - --m-feature-metadata-file
+            argument: METADATA...
+            description: The feature metadata (useful to manipulate the arrows in the plot).
+          - names:
+              - --p-ignore-missing-samples
+              - --p-no-ignore-missing-samples
+            argument: ""
+            description: 'This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]'
+          - names:
+              - --p-invert
+              - --p-no-invert
+            argument: ""
+            description: 'If specified, the point and arrow coordinates will be swapped. [default: False]'
+          - names:
+              - --p-number-of-features
+            argument: ""
+            description: INTEGER
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: plot
+        description: Visualize and Interact with Principal Coordinates Analysis
+        usage: qiime emperor plot [OPTIONS]
+        options:
+          - names:
+              - --i-pcoa
+            argument: ARTIFACT
+            description: The principal coordinates matrix to be plotted. [required]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata. [required]
+          - names:
+              - --p-ignore-missing-samples
+              - --p-no-ignore-missing-samples
+            argument: ""
+            description: 'This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]'
+          - names:
+              - --p-ignore-pcoa-features
+              - --p-no-ignore-pcoa-features
+            argument: ""
+            description: 'Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the `biplot` method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised. [default: False]'
+          - names:
+              - --p-custom-axes
+            argument: TEXT...
+            description: Numeric sample metadata columns that should be included as axes in the Emperor plot.
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: procrustes-plot
+        description: Visualize and Interact with a procrustes plot
+        usage: qiime emperor procrustes-plot [OPTIONS]
+        options:
+          - names:
+              - --i-reference-pcoa
+            argument: ARTIFACT
+            description: The reference ordination matrix to be plotted. [required]
+          - names:
+              - --i-other-pcoa
+            argument: ARTIFACT
+            description: The "other" ordination matrix to be plotted (the one that was fitted to the reference). [required]
+          - names:
+              - --i-m2-stats
+            argument: ARTIFACT ProcrustesStatistics
+            description: The M^2 value of the procrustes analysis & its associated p value. [optional]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata. [required]
+          - names:
+              - --p-custom-axes
+            argument: TEXT...
+            description: Numeric sample metadata columns that should be included as axes in the Emperor plot.
+          - names:
+              - --p-ignore-missing-samples
+              - --p-no-ignore-missing-samples
+            argument: ""
+            description: 'This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]'
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+  - name: feature-classifier
+    description: Plugin for taxonomic classification.
+    usage: qiime feature-classifier [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: blast
+        description: BLAST+ local alignment search.
+        usage: qiime feature-classifier blast [OPTIONS]
+        options:
+          - names:
+              - --i-query
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Query sequences. [required]
+          - names:
+              - --i-reference-reads
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Reference sequences. Incompatible with blastdb.
+          - names:
+              - --i-blastdb
+            argument: ARTIFACT
+            description: BLAST indexed database. Incompatible with
+          - names:
+              - --p-maxaccepts
+            argument: INTEGER
+            description: Maximum number of hits to keep for each query.
+          - names:
+              - --p-perc-identity
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: Reject match if percent identity to query is lower.
+          - names:
+              - --p-query-cov
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: 'Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn''s qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. [default: 0.8]'
+          - names:
+              - --p-strand
+            argument: TEXT Choices('both', 'plus', 'minus')
+            description: 'Align against reference sequences in forward ("plus"), reverse ("minus"), or both directions ("both"). [default: ''both'']'
+          - names:
+              - --p-evalue
+            argument: NUMBER
+            description: 'BLAST expectation value (E) threshold for saving hits. [default: 0.001]'
+          - names:
+              - --p-output-no-hits
+              - --p-no-output-no-hits
+            argument: ""
+            description: 'Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. Set to FALSE to mirror default BLAST search.'
+          - names:
+              - --p-num-threads
+            argument: NTHREADS
+            description: Number of threads (CPUs) to use in the BLAST search. Pass 0 to use all available CPUs.
+          - names:
+              - --o-search-results
+            argument: ARTIFACT
+            description: FeatureData[BLAST6] Top hits for each query. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: classify-consensus-blast
+        description: BLAST+ consensus taxonomy classifier
+        usage: qiime feature-classifier classify-consensus-blast [OPTIONS]
+        options:
+          - names:
+              - --i-query
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Query sequences. [required]
+          - names:
+              - --i-reference-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: reference taxonomy labels. [required]
+          - names:
+              - --i-blastdb
+            argument: ARTIFACT
+            description: BLAST indexed database. Incompatible with
+          - names:
+              - --i-reference-reads
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Reference sequences. Incompatible with blastdb.
+          - names:
+              - --p-maxaccepts
+            argument: INTEGER
+            description: Maximum number of hits to keep for each query.
+          - names:
+              - --p-perc-identity
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: Reject match if percent identity to query is lower.
+          - names:
+              - --p-query-cov
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: 'Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn''s qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. [default: 0.8]'
+          - names:
+              - --p-strand
+            argument: TEXT Choices('both', 'plus', 'minus')
+            description: 'Align against reference sequences in forward ("plus"), reverse ("minus"), or both directions ("both"). [default: ''both'']'
+          - names:
+              - --p-evalue
+            argument: NUMBER
+            description: 'BLAST expectation value (E) threshold for saving hits. [default: 0.001]'
+          - names:
+              - --p-output-no-hits
+              - --p-no-output-no-hits
+            argument: ""
+            description: 'Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. Set to FALSE to mirror default BLAST search.'
+          - names:
+              - --p-min-consensus
+            argument: NUMBER
+            description: Minimum fraction of assignments must match top hit to be accepted as consensus assignment.
+          - names:
+              - --p-unassignable-label
+            argument: TEXT
+            description: Annotation given to sequences without any hits.
+          - names:
+              - --p-num-threads
+            argument: NTHREADS
+            description: Number of threads (CPUs) to use in the BLAST search. Pass 0 to use all available CPUs.
+          - names:
+              - --o-classification
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomy classifications of query sequences.
+          - names:
+              - --o-search-results
+            argument: ARTIFACT
+            description: FeatureData[BLAST6] Top hits for each query. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: classify-consensus-vsearch
+        description: VSEARCH-based consensus taxonomy classifier
+        usage: "qiime feature-classifier classify-consensus-vsearch [OPTIONS]"
+        options:
+          - names:
+              - --i-query
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Query Sequences. [required]
+          - names:
+              - --i-reference-reads
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Reference sequences. [required]
+          - names:
+              - --i-reference-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Reference taxonomy labels. [required]
+          - names:
+              - --p-maxaccepts
+            argument: VALUE
+            description: Maximum number of hits to keep for each query.
+          - names:
+              - --p-perc-identity
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: Reject match if percent identity to query is lower.
+          - names:
+              - --p-query-cov
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: 'Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8]'
+          - names:
+              - --p-strand
+            argument: TEXT Choices('both', 'plus')
+            description: Align against reference sequences in forward ("plus") or both directions ("both").
+          - names:
+              - --p-search-exact
+              - --p-no-search-exact
+            argument: ""
+            description: 'Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity, query-cov, maxaccepts, and maxrejects settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False]'
+          - names:
+              - --p-top-hits-only
+              - --p-no-top-hits-only
+            argument: ""
+            description: 'Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False]'
+          - names:
+              - --p-maxhits
+            argument: VALUE
+            description: Maximum number of hits to show once the search is terminated.
+          - names:
+              - --p-maxrejects
+            argument: VALUE
+            description: Maximum number of non-matching target sequences to consider before stopping the search.
+          - names:
+              - --p-output-no-hits
+              - --p-no-output-no-hits
+            argument: ""
+            description: 'Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs.'
+          - names:
+              - --p-weak-id
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: 'Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0]'
+          - names:
+              - --p-threads
+            argument: NTHREADS
+            description: 'Number of threads to use for job parallelization. Pass 0 to use one per available CPU. [default: 1]'
+          - names:
+              - --p-min-consensus
+            argument: NUMBER
+            description: Minimum fraction of assignments must match top hit to be accepted as consensus assignment.
+          - names:
+              - --p-unassignable-label
+            argument: TEXT
+            description: Annotation given to sequences without any hits.
+          - names:
+              - --o-classification
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomy classifications of query sequences. [required]
+          - names:
+              - --o-search-results
+            argument: ARTIFACT
+            description: FeatureData[BLAST6] Top hits for each query. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: classify-hybrid-vsearch-sklearn
+        description: 'ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier'
+        usage: qiime feature-classifier classify-hybrid-vsearch-sklearn
+        options:
+          - names:
+              - --i-query
+            argument: ARTIFACT
+            description: Query Sequences. [required]
+          - names:
+              - --i-reference-reads
+            argument: ARTIFACT
+            description: Reference sequences. [required]
+          - names:
+              - --i-reference-taxonomy
+            argument: ARTIFACT
+            description: Reference taxonomy labels. [required]
+          - names:
+              - --i-classifier
+            argument: ARTIFACT
+            description: Pre-trained sklearn taxonomic classifier for classifying the reads. [required]
+          - names:
+              - --p-maxaccepts
+            argument: VALUE
+            description: 'Maximum number of hits to keep for each query. Set to "all" to keep all hits > perc-identity similarity. Note that if strand=both, maxaccepts will keep N hits for each direction (if searches in the opposite direction yield results that exceed the minimum perc-identity). In those cases use maxhits to control the total number of hits returned. This option works in pair with maxrejects. The search process sorts target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if the first target sequence passes the acceptation criteria, it is accepted as best hit and the search process stops for that query. If maxaccepts is set to a higher value, more hits are accepted. If maxaccepts and maxrejects are both set to "all", the complete database is searched. [default: 10]'
+          - names:
+              - --p-perc-identity
+            argument: PROPORTION
+            description: 'Percent sequence similarity to use for PREFILTER. Reject match if percent identity to query is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.5]'
+          - names:
+              - --p-query-cov
+            argument: PROPORTION
+            description: 'Query coverage threshold to use for PREFILTER. Reject match if query alignment coverage per high-scoring pair is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.8]'
+          - names:
+              - --p-strand
+            argument: '{''both'', ''plus''}'
+            description: 'Align against reference sequences in forward ("plus") or both directions ("both"). [default: ''both'']'
+          - names:
+              - --p-min-consensus
+            argument: NUMBER
+            description: Minimum fraction of assignments must match top hit to be accepted as consensus assignment.
+          - names:
+              - --p-maxhits
+            argument: VALUE
+            description: 'max hits [default: ''all'']'
+          - names:
+              - --p-maxrejects
+            argument: VALUE
+            description: 'max rejects [default: ''all'']'
+          - names:
+              - --p-reads-per-batch
+            argument: VALUE
+            description: 'Number of reads to process in each batch for sklearn classification. If "auto", this parameter is autoscaled to min(number of query sequences / threads, 20000). [default: ''auto'']'
+          - names:
+              - --p-confidence
+            argument: VALUE Float
+            description: Confidence threshold for limiting taxonomic depth. Set to "disable" to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments.
+          - names:
+              - --p-read-orientation
+            argument: '{''same'', ''reverse-complement'', ''auto''}'
+            description: 'Direction of reads with respect to reference sequences in pre-trained sklearn classifier. same will cause reads to be classified unchanged; reverse-complement will cause reads to be reversed and complemented prior to classification. "auto" will autodetect orientation based on the confidence estimates for the first 100 reads. [default: ''auto'']'
+          - names:
+              - --p-threads
+            argument: INTEGER
+            description: 'Number of threads to use for job parallelization. [default: 1]'
+          - names:
+              - --p-prefilter
+              - --p-no-prefilter
+            argument: ""
+            description: 'Toggle positive filter of query sequences on or off. [default: True]'
+          - names:
+              - --p-sample-size
+            argument: INTEGER
+            description: 'Randomly extract the given number of sequences from the reference database to use for prefiltering. This parameter is ignored if `prefilter` is disabled. [default: 1000]'
+          - names:
+              - --p-randseed
+            argument: INTEGER
+            description: Use integer as a seed for the pseudo-random
+          - names:
+              - --o-classification
+            argument: ARTIFACT
+            description: Taxonomy classifications of query sequences. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: classify-sklearn
+        description: Pre-fitted sklearn-based taxonomy classifier
+        usage: qiime feature-classifier classify-sklearn [OPTIONS]
+        options:
+          - names:
+              - --i-reads
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The feature data to be classified. [required]
+          - names:
+              - --i-classifier
+            argument: ARTIFACT
+            description: TaxonomicClassifier The taxonomic classifier for classifying the reads.
+          - names:
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]'
+          - names:
+              - --p-pre-dispatch
+            argument: TEXT
+            description: '"all" or expression, as in "3*n_jobs". The number of batches (of tasks) to be pre-dispatched.'
+          - names:
+              - --p-read-orientation
+            argument: TEXT Choices('same', 'reverse-complement', 'auto')
+            description: Direction of reads with respect to reference sequences. same will cause reads to be classified unchanged; reverse-complement will cause reads to be reversed and complemented prior to classification. "auto" will autodetect orientation based on the confidence estimates for the first 100 reads.
+          - names:
+              - --o-classification
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: extract-reads
+        description: Extract reads from reference sequences.
+        usage: qiime feature-classifier extract-reads [OPTIONS]
+        options:
+          - names:
+              - --i-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: '[required]'
+          - names:
+              - --p-f-primer
+            argument: TEXT
+            description: forward primer sequence (5' -> 3'). [required]
+          - names:
+              - --p-r-primer
+            argument: TEXT
+            description: reverse primer sequence (5' -> 3'). Do not use reverse-complemented primer sequence. [required]
+          - names:
+              - --p-trim-right
+            argument: INTEGER
+            description: 'trim-right nucleotides are removed from the 3'' end if trim-right is positive. Applied before trunc-len and trim-left. [default: 0]'
+          - names:
+              - --p-trunc-len
+            argument: INTEGER
+            description: read is cut to trunc-len if trunc-len is positive. Applied after trim-right but before trim-left.
+          - names:
+              - --p-trim-left
+            argument: INTEGER
+            description: 'trim-left nucleotides are removed from the 5'' end if trim-left is positive. Applied after trim-right and trunc-len. [default: 0]'
+          - names:
+              - --p-identity
+            argument: NUMBER
+            description: minimum combined primer match identity threshold.
+          - names:
+              - --p-min-length
+            argument: INTEGER
+            description: Minimum amplicon length. Shorter amplicons are
+          - names:
+              - --p-max-length
+            argument: INTEGER
+            description: Maximum amplicon length. Longer amplicons are
+          - names:
+              - --p-n-jobs
+            argument: INTEGER
+            description: Number of seperate processes to run.
+          - names:
+              - --p-read-orientation
+            argument: TEXT Choices('both', 'forward', 'reverse')
+            description: 'Orientation of primers relative to the sequences: "forward" searches for primer hits in the forward direction, "reverse" searches reverse-complement, and "both" searches both directions.'
+          - names:
+              - --o-reads
+            argument: ARTIFACT FeatureData[Sequence]
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: find-consensus-annotation
+        description: Find consensus among multiple annotations.
+        usage: qiime feature-classifier find-consensus-annotation [OPTIONS]
+        options:
+          - names:
+              - --i-search-results
+            argument: ARTIFACT FeatureData[BLAST6]
+            description: Search results in BLAST6 output format [required]
+          - names:
+              - --i-reference-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: reference taxonomy labels. [required]
+          - names:
+              - --p-unassignable-label
+            argument: TEXT
+            description: Annotation given when no consensus is found.
+          - names:
+              - --o-consensus-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Consensus taxonomy and scores. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: fit-classifier-naive-bayes
+        description: Train the naive_bayes classifier
+        usage: "qiime feature-classifier fit-classifier-naive-bayes \n    [OPTIONS]"
+        options:
+          - names:
+              - --i-reference-reads
+            argument: ARTIFACT FeatureData[Sequence]
+            description: '[required]'
+          - names:
+              - --i-reference-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: '[required]'
+          - names:
+              - --i-class-weight
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: '[optional]'
+          - names:
+              - --p-classify--alpha
+            argument: NUMBER
+            description: '[default: 0.001]'
+          - names:
+              - --p-classify--chunk-size
+            argument: INTEGER
+            description: '[default: 20000]'
+          - names:
+              - --p-classify--fit-prior
+              - --p-no-classify--fit-prior
+            argument: ""
+            description: '[default: False]'
+          - names:
+              - --p-feat-ext--alternate-sign
+              - --p-no-feat-ext--alternate-sign
+            argument: ""
+            description: '[default: False]'
+          - names:
+              - --p-feat-ext--binary
+              - --p-no-feat-ext--binary
+            argument: ""
+            description: '[default: False]'
+          - names:
+              - --p-verbose
+              - --p-no-verbose
+            argument: ""
+            description: '[default: False]'
+          - names:
+              - --p-classify--class-prior
+            argument: TEXT
+            description: '[default: ''null'']'
+          - names:
+              - --p-feat-ext--analyzer
+            argument: TEXT
+            description: '[default: ''char_wb'']'
+          - names:
+              - --p-feat-ext--preprocessor
+            argument: TEXT
+            description: '[default: ''null'']'
+          - names:
+              - --p-feat-ext--stop-words
+            argument: TEXT
+            description: '[default: ''null'']'
+          - names:
+              - --p-feat-ext--strip-accents
+            argument: TEXT
+            description: '[default: ''null'']'
+          - names:
+              - --p-feat-ext--tokenizer
+            argument: TEXT
+            description: '[default: ''null'']'
+          - names:
+              - --p-feat-ext--decode-error
+            argument: TEXT
+            description: '[default: ''strict'']'
+          - names:
+              - --p-feat-ext--encoding
+            argument: TEXT
+            description: '[default: ''utf-8'']'
+          - names:
+              - --p-feat-ext--input
+            argument: TEXT
+            description: '[default: ''content'']'
+          - names:
+              - --p-feat-ext--lowercase
+              - --p-no-feat-ext--lowercase
+            argument: ""
+            description: '[default: True]'
+          - names:
+              - --p-feat-ext--n-features
+            argument: INTEGER
+            description: '[default: 8192]'
+          - names:
+              - --p-feat-ext--ngram-range
+            argument: TEXT
+            description: '[default: ''[7, 7]'']'
+          - names:
+              - --p-feat-ext--norm
+            argument: TEXT
+            description: '[default: ''l2'']'
+          - names:
+              - --p-feat-ext--token-pattern
+            argument: TEXT
+            description: '[default: ''(?u)\\b\\w\\w+\\b'']'
+          - names:
+              - --o-classifier
+            argument: ARTIFACT TaxonomicClassifier
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: fit-classifier-sklearn
+        description: Train an almost arbitrary scikit-learn classifier
+        usage: qiime feature-classifier fit-classifier-sklearn [OPTIONS]
+        options:
+          - names:
+              - --i-reference-reads
+            argument: ARTIFACT FeatureData[Sequence]
+            description: '[required]'
+          - names:
+              - --i-reference-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: '[required]'
+          - names:
+              - --i-class-weight
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: '[optional]'
+          - names:
+              - --p-classifier-specification
+            argument: TEXT
+            description: '[required]'
+          - names:
+              - --o-classifier
+            argument: ARTIFACT TaxonomicClassifier
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: makeblastdb
+        description: Make BLAST database.
+        usage: qiime feature-classifier makeblastdb [OPTIONS]
+        options:
+          - names:
+              - --i-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Input reference sequences. [required]
+          - names:
+              - --o-database
+            argument: ARTIFACT
+            description: Output BLAST database.
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: vsearch-global
+        description: VSEARCH global alignment search
+        usage: qiime feature-classifier vsearch-global [OPTIONS]
+        options:
+          - names:
+              - --i-query
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Query Sequences. [required]
+          - names:
+              - --i-reference-reads
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Reference sequences. [required]
+          - names:
+              - --p-perc-identity
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: Reject match if percent identity to query is lower.
+          - names:
+              - --p-query-cov
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: 'Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8]'
+          - names:
+              - --p-strand
+            argument: TEXT Choices('both', 'plus')
+            description: Align against reference sequences in forward ("plus") or both directions ("both").
+          - names:
+              - --p-search-exact
+              - --p-no-search-exact
+            argument: ""
+            description: 'Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity, query-cov, maxaccepts, and maxrejects settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False]'
+          - names:
+              - --p-top-hits-only
+              - --p-no-top-hits-only
+            argument: ""
+            description: 'Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False]'
+          - names:
+              - --p-output-no-hits
+              - --p-no-output-no-hits
+            argument: ""
+            description: 'Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs.'
+          - names:
+              - --p-weak-id
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: 'Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0]'
+          - names:
+              - --p-threads
+            argument: NTHREADS
+            description: 'Number of threads to use for job parallelization. Pass 0 to use one per available CPU. [default: 1]'
+          - names:
+              - --o-search-results
+            argument: ARTIFACT
+            description: FeatureData[BLAST6] Top hits for each query. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+  - name: feature-table
+    description: Plugin for working with sample by feature tables.
+    usage: qiime feature-table [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: core-features
+        description: Identify core features in table
+        usage: qiime feature-table core-features [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table to use in core features calculations. [required]
+          - names:
+              - --p-min-fraction
+            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
+            description: 'The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 0.5]'
+          - names:
+              - --p-max-fraction
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: 'The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 1.0]'
+          - names:
+              - --p-steps
+            argument: INTEGER
+            description: The number of steps to take between `min-fraction` and
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: filter-features
+        description: Filter features from table
+        usage: qiime feature-table filter-features [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table from which features should be filtered. [required]
+          - names:
+              - --p-min-frequency
+            argument: INTEGER
+            description: 'The minimum total frequency that a feature must have to be retained. [default: 0]'
+          - names:
+              - --p-max-frequency
+            argument: INTEGER
+            description: The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]
+          - names:
+              - --p-min-samples
+            argument: INTEGER
+            description: 'The minimum number of samples that a feature must be observed in to be retained. [default: 0]'
+          - names:
+              - --p-max-samples
+            argument: INTEGER
+            description: The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied). [optional]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: Feature metadata used with `where` parameter when selecting features to retain, or with `exclude-ids` when selecting features to discard.
+          - names:
+              - --p-where
+            argument: TEXT
+            description: SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the feature table will be retained. [optional]
+          - names:
+              - --p-exclude-ids
+              - --p-no-exclude-ids
+            argument: ""
+            description: 'If true, the features selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. [default: False]'
+          - names:
+              - --p-filter-empty-samples
+              - --p-no-filter-empty-samples
+            argument: ""
+            description: 'If true, drop any samples where none of the retained features are present. [default: True]'
+          - names:
+              - --p-allow-empty-table
+              - --p-no-allow-empty-table
+            argument: ""
+            description: 'If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]'
+          - names:
+              - --o-filtered-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting feature table filtered by feature. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: filter-features-conditionally
+        description: Filter features from a table based on abundance and prevalence
+        usage: qiime feature-table filter-features-conditionally [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT
+            description: The feature table from which features should be filtered. [required]
+          - names:
+              - --p-abundance
+            argument: PROPORTION
+            description: The minimum relative abundance for a feature to be retained. [required]
+          - names:
+              - --p-prevalence
+            argument: PROPORTION
+            description: The minimum portion of samples that a feature must have a relative abundance of at least `abundance` to be retained. [required]
+          - names:
+              - --p-allow-empty-table
+              - --p-no-allow-empty-table
+            argument: ""
+            description: 'If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]'
+          - names:
+              - --o-filtered-table
+            argument: ARTIFACT
+            description: The resulting feature table filtered by feature. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: filter-samples
+        description: Filter samples from table
+        usage: qiime feature-table filter-samples [OPTIONS]
+        options:
+          - names:
+            - --i-table
+            argument: ARTIFACT
+            description: The feature table from which samples should be filtered. [required]
+          - names:
+              - --p-min-frequency
+            argument: INTEGER
+            description: 'The minimum total frequency that a sample must have to be retained. [default: 0]'
+          - names:
+              - --p-max-frequency
+            argument: INTEGER
+            description: The maximum total frequency that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]
+          - names:
+              - --p-min-features
+            argument: INTEGER
+            description: 'The minimum number of features that a sample must have to be retained. [default: 0]'
+          - names:
+              - --p-max-features
+            argument: INTEGER
+            description: The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied). [optional]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude-ids` when selecting samples to discard.
+          - names:
+              - --p-where
+            argument: TEXT
+            description: SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. [optional]
+          - names:
+              - --p-exclude-ids
+              - --p-no-exclude-ids
+            argument: ""
+            description: 'If true, the samples selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. [default: False]'
+          - names:
+              - --p-filter-empty-features
+              - --p-no-filter-empty-features
+            argument: ""
+            description: 'If true, features which are not present in any retained samples are dropped. [default: True]'
+          - names:
+              - --p-allow-empty-table
+              - --p-no-allow-empty-table
+            argument: ""
+            description: 'If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]'
+          - names:
+              - --o-filtered-table
+            argument: ARTIFACT
+            description: The resulting feature table filtered by sample. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: filter-seqs
+        description: Filter features from sequences
+        usage: qiime feature-table filter-seqs [OPTIONS]
+        options:
+          - names:
+              - --i-data
+            argument: ARTIFACT FeatureData[Sequence¹ | AlignedSequence²]
+            description: The sequences from which features should be filtered. [required]
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Table containing feature ids used for id-based filtering. [optional]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: Feature metadata used for id-based filtering, with `where` parameter when selecting features to retain, or with `exclude-ids` when selecting features to discard.
+          - names:
+              - --p-where
+            argument: TEXT
+            description: SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences will be retained. [optional]
+          - names:
+              - --p-exclude-ids
+              - --p-no-exclude-ids
+            argument: ""
+            description: 'If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained. [default: False]'
+          - names:
+              - --o-filtered-data
+            argument: ARTIFACT FeatureData[Sequence¹ | AlignedSequence²]
+            description: The resulting filtered sequences. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: group
+        description: Group samples or features by a metadata column
+        usage: qiime feature-table group [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The table to group samples or features on. [required]
+          - names:
+              - --p-axis
+            argument: TEXT Choices('feature', 'sample')
+            description: Along which axis to group. Each ID in the given axis must exist in `metadata`. [required]
+          - names:
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: A column defining the groups. Each unique value will become a new ID for the table on the given `axis`.
+          - names:
+              - --p-mode
+            argument: TEXT Choices('mean-ceiling', 'median-ceiling', 'sum')
+            description: How to combine samples or features within a group. `sum` will sum the frequencies across all samples or features within a group; `mean-ceiling` will take the ceiling of the mean of these frequencies; `median-ceiling` will take the ceiling of the median of these frequencies. [required]
+          - names:
+              - --o-grouped-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: A table that has been grouped along the given `axis`. IDs on that axis are replaced by values in the `metadata` column. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: heatmap
+        description: Generate a heatmap representation of a feature table
+        usage: qiime feature-table heatmap [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table to visualize. [required]
+          - names:
+              - --m-sample-metadata-file
+            argument: ""
+            description: METADATA
+          - names:
+              - --m-sample-metadata-column
+            argument: COLUMN  MetadataColumn[Categorical]
+            description: Annotate the sample IDs with these sample metadata values. When metadata is present and `cluster`='feature', samples will be sorted by the metadata values. [optional]
+          - names:
+              - --m-feature-metadata-file
+            argument: ""
+            description: METADATA
+          - names:
+              - --m-feature-metadata-column
+            argument: COLUMN  MetadataColumn[Categorical]
+            description: Annotate the feature IDs with these feature metadata values. When metadata is present and `cluster`='sample', features will be sorted by the metadata values. [optional]
+          - names:
+              - --p-normalize
+              - --p-no-normalize
+            argument: ""
+            description: Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table.
+          - names:
+              - --p-title
+            argument: TEXT
+            description: Optional custom plot title. [optional]
+          - names:
+              - --p-cluster
+            argument: TEXT Choices('both', 'features', 'none', 'samples')
+            description: 'Specify which axes to cluster. [default: ''both'']'
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: merge
+        description: Combine multiple tables
+        usage: qiime feature-table merge [OPTIONS]
+        options:
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: merge-seqs
+        description: Combine collections of feature sequences
+        usage: qiime feature-table merge-seqs [OPTIONS]
+        options:
+          - names:
+              - --i-data
+            argument: ARTIFACTS... List[FeatureData[Sequence]]
+            description: The collection of feature sequences to be merged.
+          - names:
+              - --o-merged-data
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The resulting collection of feature sequences containing all feature sequences provided. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: merge-taxa
+        description: Combine collections of feature taxonomies
+        usage: qiime feature-table merge-taxa [OPTIONS]
+        options:
+          - names:
+              - --i-data
+            argument: ARTIFACTS... List[FeatureData[Taxonomy]]
+            description: The collection of feature taxonomies to be merged.
+          - names:
+              - --o-merged-data
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: The resulting collection of feature taxonomies containing all feature taxonomies provided.
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: presence-absence
+        description: Convert to presence/absence
+        usage: qiime feature-table presence-absence [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency]
+            description: The feature table to be converted into presence/absence abundances. [required]
+          - names:
+              - --o-presence-absence-table
+            argument: ARTIFACT FeatureTable[PresenceAbsence]
+            description: The resulting presence/absence feature table.
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: rarefy
+        description: Rarefy table
+        usage: qiime feature-table rarefy [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table to be rarefied. [required]
+          - names:
+              - --p-sampling-depth
+            argument: INTEGER
+            description: The total frequency that each sample should be rarefied to. [required]
+          - names:
+              - --p-with-replacement
+              - --p-no-with-replacement
+            argument: ""
+            description: 'Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]'
+          - names:
+              - --o-rarefied-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting rarefied feature table. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: relative-frequency
+        description: Convert to relative frequencies
+        usage: qiime feature-table relative-frequency [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table to be converted into relative frequencies. [required]
+          - names:
+              - --o-relative-frequency-table
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: The resulting relative frequency feature table.
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: rename-ids
+        description: Renames sample or feature ids in a table
+        usage: qiime feature-table rename-ids [OPTIONS]
+        options:
+          - names:
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: A metadata column defining the new ids. Each original id must map to a new unique id. If strict mode is used, then every id in the original table must have a new id.
+          - names:
+              - --p-axis
+            argument: TEXT Choices('feature', 'sample')
+            description: 'Along which axis to rename the ids. [default: ''sample'']'
+          - names:
+              - --p-strict
+              - --p-no-strict
+            argument: ""
+            description: 'Whether the naming needs to be strict (each id in the table must have a new id). Otherwise, only the ids described in `metadata` will be renamed and the others will keep their original id names. [default: False]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: split
+        description: Split one feature table into many
+        usage: qiime feature-table split [OPTIONS]
+        options:
+          - names:
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: A column defining the groups. Each unique value will define a split feature table. [required]
+          - names:
+              - --p-filter-empty-features
+              - --p-no-filter-empty-features
+            argument: ""
+            description: 'If true, features which are not present in a split feature table are dropped. [default: True]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: subsample-ids
+        description: Subsample table
+        usage: qiime feature-table subsample-ids [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The feature table to be sampled. [required]
+          - names:
+              - --p-subsampling-depth
+            argument: ""
+            description: INTEGER
+          - names:
+              - --p-axis
+            argument: TEXT Choices('sample', 'feature')
+            description: The axis to sample over. If "sample" then samples will be randomly selected to be retained. If "feature" then a random set of features will be selected to be retained. [required]
+          - names:
+              - --o-sampled-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The resulting subsampled feature table. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: summarize
+        description: Summarize table
+        usage: qiime feature-table summarize [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency | PresenceAbsence]
+            description: The feature table to be summarized. [required]
+          - names:
+              - --m-sample-metadata-file
+            argument: METADATA...
+            description: The sample metadata.
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: summarize-plus
+        description: Summarize table plus
+        usage: qiime feature-table summarize-plus [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency | PresenceAbsence]
+            description: The feature table to be summarized. [required]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: The sample metadata.
+          - names:
+              - --o-feature-frequencies
+            argument: ARTIFACT
+            description: Per-sample and total frequencies per feature. [required]
+          - names:
+              - --o-sample-frequencies
+            argument: ARTIFACT
+            description: Observed feature count and total frequencies per sample. [required]
+          - names:
+              - --o-summary
+            argument: VISUALIZATION
+            description: Visual summary of feature table [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: tabulate-feature-frequencies
+        description: Tabulate feature frequencies
+        usage: qiime feature-table tabulate-feature-frequencies [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable
+            description: The input feature table. [required]
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTableFrequency | PresenceAbsence |   RelativeFrequency
+            description: The input feature table. [required]
+          - names:
+              - --o-feature-frequencies
+            argument: ARTIFACT
+            description: ImmutableMetadata Per-sample and total frequencies per feature.
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: tabulate-sample-frequencies
+        description: Tabulate sample frequencies
+        usage: qiime feature-table tabulate-sample-frequencies [OPTIONS]
+        options:
+          - names:
+              - --i-table
+            argument: ARTIFACT FeatureTable
+            description: The input feature table. [required]
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --i-table
+            argument: ARTIFACT FeatureTableFrequency | PresenceAbsence |   RelativeFrequency
+            description: The input feature table. [required]
+          - names:
+              - --o-sample-frequencies
+            argument: ARTIFACT
+            description: ImmutableMetadata Observed feature count and total frequencies per
           - names:
               - --output-dir
             argument: PATH
@@ -2658,26 +7398,30 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: alpha-phylogenetic
-        description: Alpha diversity (phylogenetic)
-        usage: qiime diversity alpha-phylogenetic [OPTIONS]
+      - name: tabulate-seqs
+        description: View sequence associated with each feature
+        usage: qiime feature-table tabulate-seqs [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
-            description: The feature table containing the samples for which alpha diversity should be computed. [required]
+              - --i-data
+            argument: ARTIFACT FeatureData[Sequence | AlignedSequence]
+            description: The feature sequences to be tabulated. [required]
           - names:
-              - --i-phylogeny
-            argument: ARTIFACT
-            description: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. [required]
+              - --i-taxonomy
+            argument: ARTIFACTS... Collection[FeatureData[Taxonomy]]
+            description: The taxonomic classifications of the tabulated features. [optional]
           - names:
-              - --p-metric
-            argument: TEXT
-            description: The alpha diversity metric to be computed. [required]
+              - --p-merge-method
+            argument: TEXT Choices('strict', 'union', 'intersect')
+            description: 'Method that joins data sets [default: ''strict'']'
           - names:
-              - --o-alpha-diversity
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector containing per-sample alpha diversities. [required]
+              - --o-visualization
+            argument: VISUALIZATION
+            description: "[required]"
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: Any additional metadata for the tabulated features.
           - names:
               - --output-dir
             argument: PATH
@@ -2687,26 +7431,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -2719,42 +7443,10 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: alpha-rarefaction
-        description: Alpha rarefaction curves
-        usage: qiime diversity alpha-rarefaction [OPTIONS]
+      - name: transpose
+        description: Transpose a feature table.
+        usage: qiime feature-table transpose [OPTIONS]
         options:
-          - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Feature table to compute rarefaction curves from. [required]
-          - names:
-              - --i-phylogeny
-            argument: ARTIFACT
-            description: Optional phylogeny for phylogenetic metrics.
-          - names:
-              - --p-max-depth
-            argument: INTEGER
-            description: The maximum rarefaction depth. Must be greater than min-depth. [required]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata.
-          - names:
-              - --p-min-depth
-            argument: INTEGER
-            description: The minimum rarefaction depth.
-          - names:
-              - --p-steps
-            argument: INTEGER
-            description: 'The number of rarefaction depths to include between min-depth and max-depth. [default: 10]'
-          - names:
-              - --p-iterations
-            argument: INTEGER
-            description: 'The number of rarefied feature tables to compute at each step. [default: 10]'
-          - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -2776,30 +7468,43 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: beta
-        description: Beta diversity
-        usage: qiime diversity beta [OPTIONS]
+  - name: fondue
+    description: Plugin for fetching sequences and metadata.
+    usage: qiime fondue [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: combine-seqs
+        description: Combine sequences from multiple artifacts.
+        usage: qiime fondue combine-seqs [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: 'ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]'
-            description: The feature table containing the samples over which beta diversity should be computed. [required]
-          - names:
-              - --p-metric
-            argument: '{aitchison, braycurtis, canberra, canberra_adkins, chebyshev, cityblock, correlation, cosine, dice, euclidean, hamming, jaccard, jensenshannon, kulsinski, matching, minkowski, rogerstanimoto, russellrao, seuclidean, sokalmichener, sokalsneath, sqeuclidean, yule}'
-            description: The beta diversity metric to be computed.
-          - names:
-              - --p-pseudocount
-            argument: INTEGER
-            description: A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics.
+            - --i-seqs
+            argument: ARTIFACT...
+            description: Sequence artifacts to be combined together. [required]
           - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = ''auto'', one job will be launched for each identified CPU core on the host. [default: 1]'
+              - --p-on-duplicates
+            argument: TEXT Choices('error', 'warn')
+            description: 'Preferred behaviour when duplicated sequence IDs are encountered: "warn" displays a warning and continues to combining deduplicated samples while "error" raises an error and aborts further execution. [default: ''error'']'
           - names:
-              - --o-distance-matrix
+              - --o-combined-seqs
             argument: ARTIFACT
-            description: DistanceMatrix The resulting distance matrix. [required]
+            description: Sequences combined from all input artifacts. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -2809,26 +7514,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -2841,52 +7526,50 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: beta-correlation
-        description: Beta diversity correlation
-        usage: qiime diversity beta-correlation [OPTIONS]
+      - name: get-all
+        description: Fetch sequence-related metadata and sequences of all run, study, BioProject, experiment or sample IDs.
+        usage: qiime fondue get-all [OPTIONS]
         options:
           - names:
-              - --i-distance-matrix
+              - --i-accession-ids
             argument: ARTIFACT
-            description: Matrix of distances between pairs of samples. [required]
+            description: Artifact containing run, study, BioProject, experiment or sample IDs for which the metadata and/or sequences should be fetched. Associated DOI names can be providedin an optional column and are preserved in get-alland get-metadata actions. [required]
           - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Numeric metadata column from which to compute pairwise Euclidean distances [required]
+              - --i-linked-doi
+            argument: ARTIFACT
+            description: Optional table containing linked DOI names that is only used if accession-ids does not contain any DOI names.
           - names:
-              - --p-method
-            argument: TEXT Choices('spearman', 'pearson')
-            description: 'The correlation test to be applied in the Mantel test. [default: ''spearman'']'
+              - --p-email
+            argument: TEXT
+            description: Your e-mail address (required by NCBI). [required]
           - names:
-              - --p-permutations
+              - --p-n-jobs
             argument: INTEGER
-            description: 'The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]'
+            description: Number of concurrent download jobs.
           - names:
-              - --p-intersect-ids
-              - --p-no-intersect-ids
-            argument: ""
-            description: 'If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]'
+              - --p-retries
+            argument: INTEGER
+            description: Number of retries to fetch sequences.
           - names:
-              - --p-label1
-            argument: TEXT
-            description: 'Label for `distance-matrix` in the output visualization. [default: ''Distance Matrix'']'
+              - --p-log-level
+            argument: TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')
+            description: 'Logging level. [default: ''INFO'']'
           - names:
-              - --p-label2
-            argument: TEXT
-            description: 'Label for `metadata-distance-matrix` in the output visualization. [default: ''Metadata'']'
+              - --o-metadata
+            argument: ARTIFACT
+            description: Table containing metadata for all the requested
           - names:
-              - --p-permutations
-            argument: INTEGER
-            description: The number of permutations to be run when computing p-values.
+              - --o-single-reads
+            argument: ARTIFACT
+            description: Artifact containing single-read fastq.gz files for all the requested IDs. [required]
           - names:
-              - --o-metadata-distance-matrix
+              - --o-paired-reads
             argument: ARTIFACT
-            description: 'The Distance Matrix produced from the metadata column and used in the mantel test [required]'
+            description: Artifact containing paired-end fastq.gz files for all the requested IDs. [required]
           - names:
-              - --o-mantel-scatter-visualization
-            argument: VISUALIZATION
-            description: 'Scatter plot rendering of the manteltest results [required]'
+              - --o-failed-runs
+            argument: ARTIFACT
+            description: List of all run IDs for which fetching sequences and/or metadata  failed, with their corresponding error messages. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -2928,36 +7611,30 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: beta-group-significance
-        description: Beta diversity group significance
-        usage: qiime diversity beta-group-significance [OPTIONS]
+      - name: get-ids-from-query
+        description: Find SRA run accession IDs based on a search query.
+        usage: qiime fondue get-ids-from-query [OPTIONS]
         options:
           - names:
-              - --i-distance-matrix
-            argument: ARTIFACT
-            description: Matrix of distances between pairs of samples.
-          - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Categorical sample metadata column. [required]
-          - names:
-              - --p-method
-            argument: TEXT Choices('permanova', 'anosim', 'permdisp')
-            description: The group significance test to be applied.
+              - --p-query
+            argument: TEXT
+            description: Search query to retrieve SRA run IDs from the BioSample database. [required]
           - names:
-              - --p-pairwise
-              - --p-no-pairwise
-            argument: ""
-            description: 'Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column. [default: False]'
+              - --p-email
+            argument: TEXT
+            description: Your e-mail address (required by NCBI). [required]
           - names:
-              - --p-permutations
+              - --p-n-jobs
             argument: INTEGER
-            description: 'The number of permutations to be run when computing p-values. [default: 999]'
+            description: Number of concurrent download jobs.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --p-log-level
+            argument: TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')
+            description: 'Logging level. [default: ''INFO'']'
+          - names:
+              - --o-ids
+            argument: ARTIFACT
+            description: Table containing metadata for all the requested IDs.  [required]
           - names:
               - --output-dir
             argument: PATH
@@ -2979,44 +7656,38 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: beta-phylogenetic
-        description: Beta diversity (phylogenetic)
-        usage: qiime diversity beta-phylogenetic [OPTIONS]
+      - name: get-metadata
+        description: Fetch sequence-related metadata based on run, study, BioProject, experiment or sample ID.
+        usage: qiime fondue get-metadata [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: 'ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]'
-            description: The feature table containing the samples over which beta diversity should be computed. [required]
-          - names:
-              - --i-phylogeny
+              - --i-accession-ids
             argument: ARTIFACT
-            description: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]
+            description: Artifact containing run, study, BioProject, experiment or sample IDs for which the metadata and/or sequences should be fetched. Associated DOI names can be providedin an optional column and are preserved in get-alland get-metadata actions.
           - names:
-              - --p-metric
-            argument: '{generalized_unifrac, unweighted_unifrac, weighted_normalized_unifrac, weighted_unifrac}'
-            description: The beta diversity metric to be computed. [required]
+              - --i-linked-doi
+            argument: ARTIFACT
+            description: Optional table containing linked DOI names that is only used if accession-ids does not contain any DOI names.
           - names:
-              - --p-threads
-            argument: NTHREADS
-            description: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.
+              - --p-email
+            argument: TEXT
+            description: Your e-mail address (required by NCBI). [required]
           - names:
-              - --p-variance-adjusted
-              - --p-no-variance-adjusted
-            argument: ""
-            description: 'Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]'
+              - --p-n-jobs
+            argument: INTEGER
+            description: Number of concurrent download jobs.
           - names:
-              - --p-alpha
-            argument: PROPORTION Range(0, 1, inclusive_end=True)
-            description: This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized. [optional]
+              - --p-log-level
+            argument: TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')
+            description: 'Logging level. [default: ''INFO'']'
           - names:
-              - --p-bypass-tips
-              - --p-no-bypass-tips
-            argument: ""
-            description: 'In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]'
+              - --o-metadata
+            argument: ARTIFACT
+            description: Table containing metadata for all the requested IDs. [required]
           - names:
-              - --o-distance-matrix
+              - --o-failed-runs
             argument: ARTIFACT
-            description: The resulting distance matrix. [required]
+            description: List of all run IDs for which fetching metadata failed, with their corresponding error messages. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -3026,26 +7697,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -3058,54 +7709,47 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: beta-rarefaction
-        description: Beta diversity rarefaction
-        usage: qiime diversity beta-rarefaction [OPTIONS]
+      - name: get-sequences
+        description: Fetch sequences based on run ID.
+        usage: qiime fondue get-sequences [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Feature table upon which to perform beta diversity rarefaction analyses. [required]
-          - names:
-              - --i-phylogeny
+              - --i-accession-ids
             argument: ARTIFACT
-            description: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required for phylogenetic metrics] [optional]
-          - names:
-              - --p-metric
-            argument: '{aitchison, braycurtis, canberra, canberra_adkins, chebyshev, cityblock, correlation, cosine, dice, euclidean, generalized_unifrac, hamming, jaccard, jensenshannon, kulsinski, matching, minkowski, rogerstanimoto, russellrao, seuclidean, sokalmichener, sokalsneath, sqeuclidean, unweighted_unifrac, weighted_normalized_unifrac, weighted_unifrac, yule}'
-            description: The beta diversity metric to be computed. [required]
+            description: Artifact containing run, study, BioProject, experiment or sample IDs for which the metadata and/or sequences should be fetched. Associated DOI names can be providedin an optional column and are preserved in get-alland get-metadata actions.
           - names:
-              - --p-clustering-method
-            argument: '{nj, upgma}'
-            description: Samples can be clustered with neighbor joining or UPGMA. An arbitrary rarefaction trial will be used for the tree, and the remaining trials are used to calculate the support of the internal nodes of that tree. [required]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata used for the Emperor jackknifed PCoA plot. [required]
+              - --p-email
+            argument: TEXT
+            description: Your e-mail address (required by NCBI). [required]
           - names:
-              - --p-sampling-depth
+              - --p-retries
             argument: INTEGER
-            description: The total frequency that each sample should be rarefied to prior to computing the diversity metric. [required]
+            description: Number of retries to fetch sequences.
           - names:
-              - --p-iterations
+              - --p-n-jobs
             argument: INTEGER
-            description: 'Number of times to rarefy the feature table at a given sampling depth. [default: 10]'
+            description: Number of concurrent download jobs.
           - names:
-              - --p-clustering-method
-            argument: TEXT Choices('nj', 'upgma')
-            description: Samples can be clustered with neighbor joining or UPGMA. An arbitrary rarefaction trial will be used for the tree, and the remaining trials are used to calculate the support of the internal nodes of that tree. [required]
+              - --p-log-level
+            argument: TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')
+            description: 'Logging level. [default: ''INFO'']'
           - names:
-              - --p-correlation-method
-            argument: TEXT Choices('pearson', 'spearman')
-            description: 'The Mantel correlation test to be applied when computing correlation between beta diversity distance matrices. [default: ''spearman'']'
+              - --p-restricted-access
+              - --p-no-restricted-access
+            argument: ""
+            description: If sequence fetch requires dbGaP repository key.
           - names:
-              - --p-color-scheme
-            argument: '{BrBG, BrBG_r, PRGn, PRGn_r, PiYG, PiYG_r, PuOr, PuOr_r, RdBu, RdBu_r, RdGy, RdGy_r, RdYlBu, RdYlBu_r, RdYlGn, RdYlGn_r}'
-            description: The matplotlib color scheme to generate the heatmap with.
+              - --o-single-reads
+            argument: ARTIFACT SampleData[SequencesWithQuality]
+            description: Artifact containing single-read fastq.gz files for all the requested IDs. [required]
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-paired-reads
+            argument: ARTIFACT SampleData[PairedEndSequencesWithQuality]
+            description: Artifact containing paired-end fastq.gz files for all the requested IDs. [required]
+          - names:
+              - --o-failed-runs
+            argument: ARTIFACT
+            description: List of all run IDs for which fetching sequences failed, with their corresponding error messages. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -3127,22 +7771,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: bioenv
-        description: bioenv
-        usage: qiime diversity bioenv [OPTIONS]
+      - name: merge-metadata
+        description: Merge several metadata files into a single metadata object.
+        usage: qiime fondue merge-metadata [OPTIONS]
         options:
           - names:
-              - --i-distance-matrix
-            argument: ARTIFACT
-            description: Matrix of distances between pairs of samples.
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata.
+              - --i-metadata
+            argument: ARTIFACTS...
+            description: Metadata files to be merged together. [required]
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-merged-metadata
+            argument: ARTIFACT
+            description: Merged metadata containing all rows and columns (without duplicates). [required]
           - names:
               - --output-dir
             argument: PATH
@@ -3164,76 +7804,42 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: core-metrics
-        description: Core diversity metrics (non-phylogenetic)
-        usage: qiime diversity core-metrics [OPTIONS]
+      - name: scrape-collection
+        description: Scrape Zotero collection for run, study, BioProject, experiment and sample IDs, and associated DOI names.
+        usage: qiime fondue scrape-collection [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table containing the samples over which diversity metrics should be computed. [required]
-          - names:
-              - --p-sampling-depth
-            argument: INTEGER
-            description: The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata to use in the emperor plots. [required]
-          - names:
-              - --p-with-replacement
-              - --p-no-with-replacement
-            argument: ""
-            description: 'Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]'
-          - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: '[beta methods only] - The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = ''auto'', one job will be launched for each identified CPU core on the host. [default: 1]'
-          - names:
-              - --p-ignore-missing-samples
-              - --p-no-ignore-missing-samples
-            argument: ""
-            description: 'If set to `True` samples and features without metadata are included by setting all metadata values to: "This element has no metadata". By default an exception will be raised if missing elements are encountered. Note, this flag only takes effect if there is at least one overlapping element.'
-          - names:
-              - --o-rarefied-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting rarefied feature table. [required]
-          - names:
-              - --o-observed-features-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector of Observed Features values by sample. [required]
+              - --p-collection-name
+            argument: TEXT
+            description: Name of the collection to be scraped. [required]
           - names:
-              - --o-shannon-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector of Shannon diversity values by sample. [required]
+              - --p-on-no-dois
+            argument: TEXT Choices('ignore', 'error')
+            description: 'Behavior if no DOIs were found. [default: ''ignore'']'
           - names:
-              - --o-evenness-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector of Pielou's evenness values by sample. [required]
+              - --p-log-level
+            argument: TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')
+            description: 'Logging level. [default: ''INFO'']'
           - names:
-              - --o-jaccard-distance-matrix
+              - --o-run-ids
             argument: ARTIFACT
-            description: Matrix of Jaccard distances between pairs of samples. [required]
+            description: Artifact containing all run IDs scraped from a Zotero collection and associated DOI names. [required]
           - names:
-              - --o-bray-curtis-distance-matrix
+              - --o-study-ids
             argument: ARTIFACT
-            description: Matrix of Bray-Curtis distances between pairs of samples. [required]
+            description: Artifact containing all study IDs scraped from a Zotero collection and associated DOI names. [required]
           - names:
-              - --o-jaccard-pcoa-results
+              - --o-bioproject-ids
             argument: ARTIFACT
-            description: PCoA matrix computed from Jaccard distances between samples. [required]
+            description: Artifact containing all BioProject IDs scraped from a Zotero collection and associated DOI names. [required]
           - names:
-              - --o-bray-curtis-pcoa-results
+              - --o-experiment-ids
             argument: ARTIFACT
-            description: PCoA matrix computed from Bray-Curtis distances Bray-Curtis. [required]
-          - names:
-              - --o-jaccard-emperor
-            argument: VISUALIZATION
-            description: Emperor plot of the PCoA matrix computed from Jaccard. [required]
+            description: Artifact containing all experiment IDs scraped from a Zotero collection and associated DOI names. [required]
           - names:
-              - --o-bray-curtis-emperor
-            argument: VISUALIZATION
-            description: Emperor plot of the PCoA matrix computed from Bray-Curtis. [required]
+              - --o-sample-ids
+            argument: ARTIFACT
+            description: Artifact containing all experiment IDs scraped from a Zotero collection and associated DOI names. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -3243,26 +7849,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -3275,99 +7861,47 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: core-metrics-phylogenetic
-        description: Core diversity metrics (phylogenetic and non-phylogenetic)
-        usage: qiime diversity core-metrics-phylogenetic [OPTIONS]
-        options:
-          - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table containing the samples over which diversity metrics should be computed. [required]
-          - names:
-              - --i-phylogeny
-            argument: ARTIFACT
-            description: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]
-          - names:
-              - --p-sampling-depth
-            argument: INTEGER
-            description: The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata to use in the emperor plots. [required]
-          - names:
-              - --p-with-replacement
-              - --p-no-with-replacement
-            argument: ""
-            description: 'Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]'
-          - names:
-              - --o-rarefied-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting rarefied feature table. [required]
-          - names:
-              - --o-faith-pd-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector of Faith PD values by sample. [required]
-          - names:
-              - --o-observed-features-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector of Observed Features values by sample. [required]
-          - names:
-              - --o-shannon-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector of Shannon diversity values by sample. [required]
-          - names:
-              - --o-evenness-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector of Pielou's evenness values by sample. [required]
-          - names:
-              - --o-unweighted-unifrac-distance-matrix
-            argument: ARTIFACT
-            description: Matrix of unweighted UniFrac distances between pairs of samples. [required]
-          - names:
-              - --o-weighted-unifrac-distance-matrix
-            argument: ARTIFACT
-            description: Matrix of weighted UniFrac distances between pairs of samples. [required]
-          - names:
-              - --o-jaccard-distance-matrix
-            argument: ARTIFACT
-            description: Matrix of Jaccard distances between pairs of samples. [required]
-          - names:
-              - --o-bray-curtis-distance-matrix
-            argument: ARTIFACT
-            description: Matrix of Bray-Curtis distances between pairs of samples. [required]
-          - names:
-              - --o-unweighted-unifrac-pcoa-results
-            argument: ARTIFACT
-            description: PCoA matrix computed from unweighted UniFrac distances between samples. [required]
-          - names:
-              - --o-weighted-unifrac-pcoa-results
-            argument: ARTIFACT
-            description: PCoA matrix computed from weighted UniFrac distances between samples. [required]
+  - name: fragment-insertion
+    description: Plugin for extending phylogenies.
+    usage: qiime fragment-insertion [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: classify-otus-experimental
+        description: 'Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.'
+        usage: "qiime fragment-insertion classify-otus-experimental [OPTIONS]"
+        options:
           - names:
-              - --o-jaccard-pcoa-results
-            argument: ARTIFACT
-            description: PCoA matrix computed from Jaccard distances between samples. [required]
+              - --i-representative-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The sequences used for a 'sepp' run to produce the 'tree'. [required]
           - names:
-              - --o-bray-curtis-pcoa-results
+              - --i-tree
             argument: ARTIFACT
-            description: PCoA matrix computed from Bray-Curtis distances samples. [required]
-          - names:
-              - --o-unweighted-unifrac-emperor
-            argument: VISUALIZATION
-            description: Emperor plot of the PCoA matrix computed from unweighted UniFrac. [required]
-          - names:
-              - --o-weighted-unifrac-emperor
-            argument: VISUALIZATION
-            description: Emperor plot of the PCoA matrix computed from weighted UniFrac. [required]
+            description: The tree resulting from inserting fragments into a
           - names:
-              - --o-jaccard-emperor
-            argument: VISUALIZATION
-            description: Emperor plot of the PCoA matrix computed from Jaccard. [required]
+              - --i-reference-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string. [required]
           - names:
-              - --o-bray-curtis-emperor
-            argument: VISUALIZATION
-            description: Emperor plot of the PCoA matrix computed from Bray-Curtis. [required]
+              - --o-classification
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomic lineages for inserted fragments. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -3377,26 +7911,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -3409,31 +7923,26 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-alpha-diversity
-        description: Filter samples from an alpha diversity metric.
-        usage: qiime diversity filter-alpha-diversity [OPTIONS]
+      - name: filter-features
+        description: Filter fragments in tree from table.
+        usage: qiime fragment-insertion filter-features [OPTIONS]
         options:
           - names:
-              - --i-alpha-diversity
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Alpha diversity sample data to filter by sample. [required]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata used to select samples to retain from the sample data (default) or select samples to exclude using the `exclude-ids` parameter. [required]
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: A feature-table which needs to filtered down to those fragments that are contained in the tree, e.g. result of a Deblur or DADA2 run. [required]
           - names:
-              - --p-where
-            argument: TEXT
-            description: SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered alpha diversity artifact. If not provided, all samples in `metadata` that are also in the input alpha diversity artifact will be retained. [optional]
+              - --i-tree
+            argument: ARTIFACT
+            description: The tree resulting from inserting fragments into a
           - names:
-              - --p-exclude-ids
-              - --p-no-exclude-ids
-            argument: ""
-            description: If `True`, the samples selected by `metadata` or the `where` parameters will be excluded from the filtered alpha diversity artifact instead of being retained.
+              - --o-filtered-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: The input table minus those fragments that were not part of the tree. This feature-table can be used for downstream analyses like phylogenetic alpha- or betadiversity computation. [required]
           - names:
-              - --o-filtered-alpha-diversity
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: '[required]'
+              - --o-removed-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Those fragments that got removed from the input table, because they were not part of the tree. This table is mainly used for quality control, e.g. to inspect the ratio of removed reads per sample from the input table. You can ignore this table for downstream analyses.
           - names:
               - --output-dir
             argument: PATH
@@ -3455,31 +7964,43 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-distance-matrix
-        description: Filter samples from a distance matrix.
-        usage: qiime diversity filter-distance-matrix [OPTIONS]
+      - name: sepp
+        description: Insert fragment sequences using SEPP into reference phylogenies.
+        usage: qiime fragment-insertion sepp [OPTIONS]
         options:
           - names:
-              - --i-distance-matrix
-            argument: ARTIFACT
-            description: Distance matrix to filter by sample. [required]
+              - --i-representative-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The sequences to insert into the reference tree.
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude-ids` when selecting samples to discard. [required]
+              - --i-reference-database
+            argument: ARTIFACT SeppReferenceDatabase
+            description: The reference database to insert the representative sequences into. [required]
           - names:
-              - --p-where
-            argument: TEXT
-            description: SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained. [optional]
+              - --p-alignment-subset-size
+            argument: INTEGER
+            description: 'Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. [default: 1000]'
           - names:
-              - --p-exclude-ids
-              - --p-no-exclude-ids
+              - --p-placement-subset-size
+            argument: INTEGER
+            description: 'The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. Further reading: https://github.com/smirarab/sepp/blob/master/tutorial/ sepp-tutorial.md#sample-datasets-default-parameters.'
+          - names:
+              - --p-threads
+            argument: NTHREADS
+            description: 'The number of threads to use. Pass 0 to use one per available core. [default: 1]'
+          - names:
+              - --p-debug
+              - --p-no-debug
             argument: ""
-            description: If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained.
+            description: 'Collect additional run information to STDOUT for debugging. Temporary directories will not be removed if run fails. [default: False]'
           - names:
-              - --o-filtered-distance-matrix
+              - --o-tree
             argument: ARTIFACT
-            description: Distance matrix filtered to include samples matching
+            description: The tree with inserted feature data.
+          - names:
+              - --o-placements
+            argument: ARTIFACT
+            description: Placements Information about the feature placements within the
           - names:
               - --output-dir
             argument: PATH
@@ -3501,39 +8022,57 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: mantel
-        description: Apply the Mantel test to two distance matrices
-        usage: qiime diversity mantel [OPTIONS]
+  - name: longitudinal
+    description: Plugin for paired sample and time series analyses.
+    usage: qiime longitudinal [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: anova
+        description: ANOVA test
+        usage: qiime longitudinal anova [OPTIONS]
         options:
           - names:
-              - --i-dm1
-            argument: ARTIFACT
-            description: Matrix of distances between pairs of samples. [required]
-          - names:
-              - --i-dm2
-            argument: ARTIFACT
-            description: Matrix of distances between pairs of samples. [required]
+            - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata containing formula terms. [required]
           - names:
-              - --p-method
-            argument: '{spearman, pearson}'
-            description: The correlation test to be applied in the Mantel test.
+              - --p-formula
+            argument: TEXT
+            description: R-style formula specifying the model. All terms must be present in the sample metadata or metadata-transformable artifacts and can be continuous or categorical metadata columns. Formulae will be in the format "a ~ b + c", where "a" is the metric (dependent variable) and "b" and "c" are independent covariates. Use "+" to add a variable; "+ a:b" to add an interaction between variables a and b; "*" to include a variable and all interactions; and "-" to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [required]
           - names:
-              - --p-permutations
-            argument: INTEGER
-            description: The number of permutations to be run when computing p-values.
+              - --p-sstype
+            argument: TEXT Choices('I', 'II', 'III')
+            description: 'Type of sum of squares calculation to perform (I, II, or III). [default: ''II'']'
           - names:
-              - --p-intersect-ids
-              - --p-no-intersect-ids
+              - --p-repeated-measures
+              - --p-no-repeated-measures
             argument: ""
-            description: 'If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]'
+            description: 'Perform ANOVA as a repeated measures ANOVA. Implemented via statsmodels, which has the following limitations: Currently, only fully balanced within-subject designs are supported. Calculation of between-subject effects and corrections for violation of sphericity are not yet implemented. [default: False]'
           - names:
-              - --p-label1
+              - --p-individual-id-column
             argument: TEXT
-            description: Label for `dm1` in the output visualization.
+            description: The column containing individual ID with repeated measures to account for.This should not be included in the formula. [optional]
           - names:
-              - --p-label2
-            argument: TEXT
-            description: Label for `dm2` in the output visualization.
+              - --p-rm-aggregate
+              - --p-no-rm-aggregate
+            argument: ""
+            description: 'If the data set contains more than a single observation per individual id and cell of the specified model, this function will be used to aggregate the data by the mean before running the ANOVA. Only applicable for repeated measures ANOVA. [default: False]'
           - names:
               - --o-visualization
             argument: VISUALIZATION
@@ -3559,71 +8098,83 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: partial-procrustes
-        description: Partial Procrustes
-        usage: qiime diversity partial-procrustes [OPTIONS]
+      - name: feature-volatility
+        description: Feature volatility analysis
+        usage:  qiime longitudinal feature-volatility [OPTIONS]
         options:
           - names:
-              - --i-reference
-            argument: ARTIFACT
-            description: The ordination matrix to which data is fitted to. [required]
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Feature table containing all features that should be used for target prediction. [required]
           - names:
-              - --i-other
-            argument: ARTIFACT
-            description: The ordination matrix that's fitted to the reference ordination. [required]
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata file containing individual-id-column. [required]
           - names:
-              - --m-pairing-file
-            argument: METADATA
-            description: The metadata file.
+              - --p-state-column
+            argument: TEXT
+            description: Metadata containing collection time (state) values for each sample. Must contain exclusively numeric values. [required]
           - names:
-              - --m-pairing-column
-            argument: COLUMN
-            description: The metadata column describing sample pairs which exist. [required]
+              - --p-individual-id-column
+            argument: TEXT
+            description: Metadata column containing IDs for individual subjects. [optional]
           - names:
-              - --p-dimensions
+              - --p-cv
             argument: INTEGER
-            description: The number of dimensions to use when fitting the two matrices of the reference ordination. [required]
+            description: Number of k-fold cross-validations to perform.
           - names:
-              - --o-transformed
-            argument: ARTIFACT
-            description: The 'other' ordination transformed into the space of the reference ordination. [required]
+              - --p-random-state
+            argument: INTEGER
+            description: Seed used by random number generator. [optional]
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'Number of jobs to run in parallel. [default: 1]'
           - names:
-              - --verbose
-              - --quiet
+              - --p-n-estimators
+            argument: INTEGER
+            description: Number of trees to grow for estimation. More trees will improve predictive accuracy up to a threshold level, but will also increase time and memory requirements.
+          - names:
+              - --p-estimator
+            argument: '{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor, ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}'
+            description: Estimator method to use for sample prediction.
+          - names:
+              - --p-parameter-tuning
+              - --p-no-parameter-tuning
             argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
           - names:
-              - --citations
-            argument: ""
-            description: Show citations and exit.
+              - --p-importance-threshold
+            argument: VALUE
+            description: Filter feature table to exclude any features with an importance score less than this threshold.
           - names:
-              - --help
-            argument: ""
-            description: Show this message and exit.
-      - name: pcoa
-        description: Principal Coordinate Analysis
-        usage: qiime diversity pcoa [OPTIONS]
-        options:
+              - --p-feature-count
+            argument: VALUE
+            description: Filter feature table to include top N most important features.
           - names:
-              - --i-distance-matrix
-            argument: ARTIFACT
-            description: The distance matrix on which PCoA should be computed. [required]
+              - --o-filtered-table
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: Feature table containing only important features. [required]
           - names:
-              - --p-number-of-dimensions
-            argument: INTEGER
-            description: Dimensions to reduce the distance matrix to. This number determines how many eigenvectors and eigenvalues are returned,and influences the choice of algorithm used to compute them. By default, uses the default eigendecomposition method, SciPy's eigh, which computes all eigenvectors and eigenvalues in an exact manner. For very large matrices, this is expected to be slow. If a value is specified for this parameter, then the fast, heuristic eigendecomposition algorithm fsvd is used, which only computes and returns the number of dimensions specified, but suffers some degree of accuracy loss, the magnitude of which varies across different datasets. [optional]
+              - --o-feature-importance
+            argument: ARTIFACT FeatureData[Importance]
+            description: Importance of each input feature to model accuracy. [required]
           - names:
-              - --o-pcoa
-            argument: ARTIFACT
-            description: The resulting PCoA matrix.
+              - --o-volatility-plot
+            argument: VISUALIZATION
+            description: Interactive volatility plot visualization. [required]
+          - names:
+              - --o-accuracy-results
+            argument: VISUALIZATION
+            description: Accuracy results visualization. [required]
+          - names:
+              - --o-sample-estimator
+            argument: ARTIFACT SampleEstimator[Regressor]
+            description: Trained sample regressor. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -3634,42 +8185,25 @@ subcommands:
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
           - names:
-              - --citations
+              - --no-recycle
             argument: ""
-            description: Show citations and exit.
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
           - names:
-              - --help
+              - --parallel
             argument: ""
-            description: Show this message and exit.
-      - name: pcoa-biplot
-        description: Principal Coordinate Analysis Biplot
-        usage: qiime diversity pcoa-biplot [OPTIONS]
-        options:
-          - names:
-              - --i-pcoa
-            argument: ARTIFACT
-            description: The PCoA where the features will be projected onto.
-          - names:
-              - --i-features
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Variables to project onto the PCoA matrix [required]
-          - names:
-              - --o-biplot
-            argument: ARTIFACT
-            description: The resulting PCoA matrix. [required]
+            description: Execute your action in parallel. This flag will use your default parallel config.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -3682,38 +8216,42 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: procrustes-analysis
-        description: Procrustes Analysis
-        usage: qiime diversity procrustes-analysis [OPTIONS]
+      - name: first-differences
+        description: Compute first differences or difference from
+        usage: qiime longitudinal first-differences [OPTIONS]
         options:
           - names:
-              - --i-reference
-            argument: ARTIFACT
-            description: The ordination matrix to which data is fitted to. [required]
+              - --i-table
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: Feature table to optionally use for computing first differences. [optional]
           - names:
-              - --i-other
-            argument: ARTIFACT
-            description: The ordination matrix that's fitted to the reference ordination. [required]
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata file containing individual-id-column. [required]
           - names:
-              - --p-dimensions
-            argument: INTEGER
-            description: 'The number of dimensions to use when fitting the two matrices [default: 5]'
+              - --p-state-column
+            argument: TEXT
+            description: Metadata column containing state (time) variable information. [required]
           - names:
-              - --p-permutations
-            argument: VALUE
-            description: 'The number of permutations to be run when computing p-values. Supplying a value of `disable` will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]'
+              - --p-individual-id-column
+            argument: TEXT
+            description: Metadata column containing IDs for individual subjects. [required]
           - names:
-              - --o-transformed-reference
-            argument: ARTIFACT
-            description: A normalized version of the "reference" ordination matrix. [required]
+              - --p-metric
+            argument: TEXT
+            description: Numerical metadata or artifact column to test.
           - names:
-              - --o-transformed-other
-            argument: ARTIFACT
-            description: A normalized and fitted version of the "other" ordination matrix. [required]
+              - --p-replicate-handling
+            argument: TEXT Choices('error', 'random', 'drop')
+            description: 'Choose how replicate samples are handled. If replicates are detected, "error" causes method to fail; "drop" will discard all replicated samples; "random" chooses one representative at random from among replicates. [default: ''error'']'
           - names:
-              - --o-disparity-results
-            argument: ARTIFACT
-            description: The sum of the squares of the pointwise differences between the two input datasets & its p value. [required]
+              - --p-baseline
+            argument: NUMBER
+            description: A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static differences instead of first differences (which are calculated if no value is given for baseline). If a "baseline" value is provided, sample differences at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]
+          - names:
+              - --o-first-differences
+            argument: ARTIFACT SampleData[FirstDifferences]
+            description: Series of first differences. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -3735,42 +8273,38 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: tsne
-        description: t-distributed stochastic neighbor embedding
-        usage: qiime diversity tsne [OPTIONS]
+      - name: first-distances
+        description: Compute first distances or distance from baseline
+        usage: qiime longitudinal first-distances [OPTIONS]
         options:
           - names:
               - --i-distance-matrix
             argument: ARTIFACT
-            description: The distance matrix on which t-SNE should be computed. [required]
-          - names:
-              - --p-number-of-dimensions
-            argument: INTEGER
-            description: Dimensions to reduce the distance matrix to. [required]
+            description: Matrix of distances between pairs of samples. [required]
           - names:
-              - --p-perplexity
-            argument: NUMBER
-            description: 'Provide the balance between local and global structure. Low values concentrate on local structure. [default: 25.0]'
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata file containing individual-id-column. [required]
           - names:
-              - --p-n-iter
-            argument: INTEGER
-            description: '[default: 1000]'
+              - --p-state-column
+            argument: TEXT
+            description: Metadata column containing state (time) variable information. [required]
           - names:
-              - --p-learning-rate
-            argument: NUMBER
-            description: 'Controls how much the weights are adjusted at each update. [default: 200.0]'
+              - --p-individual-id-column
+            argument: TEXT
+            description: Metadata column containing IDs for individual subjects. [required]
           - names:
-              - --p-early-exaggeration
+              - --p-baseline
             argument: NUMBER
-            description: 'Affects the tightness of the shown clusters. Larger values increase the distance between natural clusters in the embedded space. [default: 12.0]'
+            description: A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a "baseline" value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column.
           - names:
-              - --p-random-state
-            argument: INTEGER
-            description: Seed used by random number generator. [optional]
+              - --p-replicate-handling
+            argument: TEXT Choices('error', 'random', 'drop')
+            description: 'Choose how replicate samples are handled. If replicates are detected, "error" causes method to fail; "drop" will discard all replicated samples; "random" chooses one representative at random from among replicates. [default: ''error'']'
           - names:
-              - --o-tsne
-            argument: ARTIFACT
-            description: The resulting t-SNE matrix. [required]
+              - --o-first-distances
+            argument: ARTIFACT SampleData[FirstDifferences]
+            description: Series of first distances. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -3792,34 +8326,59 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: umap
-        description: Uniform Manifold Approximation and Projection
-        usage: qiime diversity umap [OPTIONS]
+      - name: linear-mixed-effects
+        description: Linear mixed effects modeling
+        usage: qiime longitudinal linear-mixed-effects [OPTIONS]
         options:
           - names:
-              - --i-distance-matrix
-            argument: ARTIFACT
-            description: The distance matrix on which UMAP should be computed. [required]
+              - --i-table
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: Feature table containing metric. [optional]
           - names:
-              - --p-number-of-dimensions
-            argument: INTEGER
-            description: Dimensions to reduce the distance matrix to.
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata file containing individual-id-column. [required]
           - names:
-              - --p-n-neighbors
-            argument: INTEGER
-            description: Provide the balance between local and global structure.
+              - --p-state-column
+            argument: TEXT
+            description: Metadata column containing state (time) variable information. [required]
           - names:
-              - --p-min-dist
+              - --p-individual-id-column
+            argument: TEXT
+            description: Metadata column containing IDs for individual subjects. [required]
+          - names:
+              - --p-metric
+            argument: TEXT
+            description: Dependent variable column name. Must be a column name located in the metadata or feature table files.
+          - names:
+              - --p-group-columns
+            argument: TEXT
+            description: Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine mean structure of "metric". [optional]
+          - names:
+              - --p-random-effects
+            argument: TEXT
+            description: Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine the variance and covariance structure (random effects) of "metric". To add a random slope, the same value passed to "state-column" should be passed here. A random intercept for each individual is set by default and does not need to be passed here. [optional]
+          - names:
+              - --p-palette
+            argument: TEXT
+            description: Color palette to use for generating boxplots.
+          - names:
+              - --p-lowess
+              - --p-no-lowess
+            argument: ""
+            description: 'Estimate locally weighted scatterplot smoothing. Note that this will eliminate confidence interval plotting. [default: False]'
+          - names:
+              - --p-ci
             argument: NUMBER
-            description: Controls the cluster size. Low values cause clumpier clusters.
+            description: Size of the confidence interval for the regression
           - names:
-              - --p-random-state
-            argument: INTEGER
-            description: Seed used by random number generator. [optional]
+              - --p-formula
+            argument: TEXT
+            description: R-style formula to use for model specification. A formula must be used if the "metric" parameter is None. Note that the metric and group columns specified in the formula will override metric and group columns that are passed separately as parameters to this method. Formulae will be in the format "a ~ b + c", where "a" is the metric (dependent variable) and "b" and "c" are independent covariates. Use "+" to add a variable; "+ a:b" to add an interaction between variables a and b; "*" to include a variable and all interactions; and "-" to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [optional]
           - names:
-              - --o-umap
-            argument: ARTIFACT
-            description: The resulting UMAP matrix. [required]
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -3841,88 +8400,117 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: diversity-lib
-    description: Plugin for computing community diversity.
-    usage: qiime diversity-lib [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: alpha-passthrough
-        description: Alpha Passthrough (non-phylogenetic)
-        usage: qiime diversity-lib alpha-passthrough [OPTIONS]
+      - name: maturity-index
+        description: Microbial maturity index prediction.
+        usage: qiime longitudinal maturity-index [OPTIONS]
         options:
           - names:
               - --i-table
             argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table containing the samples for which a selected metric should be computed. [required]
+            description: Feature table containing all features that should be used for target prediction. [required]
           - names:
-              - --p-metric
+              - --m-metadata-file
+            argument: METADATA...
+            description: metadata file(s) [required]
+          - names:
+              - --p-state-column
             argument: TEXT
-            description: The alpha diversity metric to be computed. [required]
+            description: Numeric metadata column containing sampling time (state) data to use as prediction target. [required]
           - names:
-              - --o-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector containing per-sample values for the chosen metric. [required]
+              - --p-group-by
+            argument: TEXT
+            description: Categorical metadata column to use for plotting and significance testing between main treatment groups. [required]
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-control
+            argument: TEXT
+            description: Value of group-by to use as control group. The regression model will be trained using only control group data, and the maturity scores of other groups consequently will be assessed relative to this group. [required]
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --p-individual-id-column
+            argument: TEXT
+            description: Optional metadata column containing IDs for individual subjects. Adds individual subject (spaghetti) vectors to volatility charts if a column name is provided. [optional]
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-estimator
+            argument: '{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor[DecisionTree], AdaBoostRegressor[ExtraTrees], ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}'
+            description: Regression model to use for prediction.
           - names:
-              - --citations
-            argument: ""
-            description: Show citations and exit.
+              - --p-n-estimators
+            argument: INTEGER
+            description: Number of trees to grow for estimation.
           - names:
-              - --help
-            argument: ""
-            description: Show this message and exit.
-      - name: beta-passthrough
-        description: Beta Passthrough (non-phylogenetic)
-        usage: qiime diversity-lib beta-passthrough [OPTIONS]
-        options:
+              - --p-test-size
+            argument: PROPORTION
+            description: Fraction of input samples to exclude from training set and use for classifier testing.
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table containing the samples over which beta diversity should be computed. [required]
+              - --p-step
+            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
+            description: If optimize-feature-selection is True, step is the percentage of features to remove at each iteration.
           - names:
-              - --p-metric
-            argument: TEXT
-            description: The beta diversity metric to be computed. [required]
+              - --p-cv
+            argument: INTEGER
+            description: Number of k-fold cross-validations to perform.
           - names:
-              - --p-pseudocount
+              - --p-random-state
             argument: INTEGER
-            description: A pseudocount to handle zeros for compositional metrics.
+            description: Seed used by random number generator. [optional]
           - names:
               - --p-n-jobs
             argument: NTHREADS
-            description: 'The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = ''auto'', one job will be launched for each identified CPU core on the host. [default: 1]'
+            description: 'Number of jobs to run in parallel. [default: 1]'
           - names:
-              - --o-distance-matrix
-            argument: ARTIFACT
-            description: DistanceMatrix The resulting distance matrix. [required]
+              - --p-parameter-tuning
+              - --p-no-parameter-tuning
+            argument: ""
+            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
+          - names:
+              - --p-optimize-feature-selection
+              - --p-no-optimize-feature-selection
+            argument: ""
+            description: Automatically optimize input feature selection using recursive feature elimination.
+          - names:
+              - --p-stratify
+              - --p-no-stratify
+            argument: ""
+            description: 'Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: False]'
+          - names:
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+          - names:
+              - --p-feature-count
+            argument: INTEGER
+            description: Filter feature table to include top N most important features.
+          - names:
+              - --o-sample-estimator
+            argument: ARTIFACT SampleEstimator[Regressor]
+            description: Trained sample estimator. [required]
+          - names:
+              - --o-feature-importance
+            argument: ARTIFACT FeatureData[Importance]
+            description: Importance of each input feature to model accuracy. [required]
+          - names:
+              - --o-predictions
+            argument: ARTIFACT SampleData[RegressorPredictions]
+            description: Predicted target values for each input sample. [required]
+          - names:
+              - --o-model-summary
+            argument: VISUALIZATION
+            description: Summarized parameter and (if enabled) feature selection information for the trained estimator. [required]
+          - names:
+              - --o-accuracy-results
+            argument: VISUALIZATION
+            description: Accuracy results visualization. [required]
+          - names:
+              - --o-maz-scores
+            argument: ARTIFACT SampleData[RegressorPredictions]
+            description: Microbiota-for-age z-score predictions. [required]
+          - names:
+              - --o-clustermap
+            argument: VISUALIZATION
+            description: Heatmap of important feature abundance at each time point in each group. [required]
+          - names:
+              - --o-volatility-plots
+            argument: VISUALIZATION
+            description: Interactive volatility plots of MAZ and maturity scores, target (column) predictions, and the sample metadata. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -3932,6 +8520,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -3944,40 +8552,30 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: beta-phylogenetic-passthrough
-        description: Beta Phylogenetic Passthrough
-        usage: qiime diversity-lib beta-phylogenetic-passthrough [OPTIONS]
+      - name: nmit
+        description: Nonparametric microbial interdependence test
+        usage: qiime longitudinal nmit [OPTIONS]
         options:
           - names:
               - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table containing the samples over which beta diversity should be computed. [required]
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: Feature table to use for microbial interdependence test. [required]
           - names:
-              - --i-phylogeny
-            argument: ARTIFACT
-            description: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. [required]
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata file containing individual-id-column. [required]
           - names:
-              - --p-metric
+              - --p-individual-id-column
             argument: TEXT
-            description: The beta diversity metric to be computed. [required]
-          - names:
-              - --p-threads
-            argument: NTHREADS
-            description: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.
-          - names:
-              - --p-variance-adjusted
-              - --p-no-variance-adjusted
-            argument: ""
-            description: 'Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]'
+            description: Metadata column containing IDs for individual subjects. [required]
           - names:
-              - --p-alpha
-            argument: PROPORTION Range(0, 1, inclusive_end=True)
-            description: This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized. [optional]
+              - --p-corr-method
+            argument: TEXT Choices('kendall', 'pearson', 'spearman')
+            description: The temporal correlation test to be applied.
           - names:
-              - --p-bypass-tips
-              - --p-no-bypass-tips
-            argument: ""
-            description: 'In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]'
+              - --p-dist-method
+            argument: TEXT Choices('fro', 'nuc')
+            description: 'Temporal distance method, see numpy.linalg.norm for details. [default: ''fro'']'
           - names:
               - --o-distance-matrix
             argument: ARTIFACT
@@ -4003,22 +8601,55 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: bray-curtis
-        description: Bray-Curtis Dissimilarity
-        usage: qiime diversity-lib bray-curtis [OPTIONS]
+      - name: pairwise-differences
+        description: Paired difference testing and boxplots
+        usage: qiime longitudinal pairwise-differences [OPTIONS]
         options:
           - names:
               - --i-table
-            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency]
-            description: The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: Feature table to optionally use for paired comparisons. [optional]
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata file containing individual-id-column. [required]
+          - names:
+              - --p-metric
+            argument: TEXT
+            description: Numerical metadata or artifact column to test. [required]
+          - names:
+              - --p-state-column
+            argument: TEXT
+            description: Metadata column containing state (e.g., Time) across which samples are paired. [required]
+          - names:
+              - --p-state-1
+            argument: TEXT
+            description: Baseline state column value. [required]
+          - names:
+              - --p-state-2
+            argument: TEXT
+            description: State column value to pair with baseline. [required]
+          - names:
+              - --p-individual-id-column
+            argument: TEXT
+            description: 'Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling="random" to instead randomly select one member. [required]'
+          - names:
+              - --p-group-column
+            argument: TEXT
+            description: Metadata column on which to separate groups for comparison [optional]
+          - names:
+              - --p-parametric
+              - --p-no-parametric
+            argument: ""
+            description: Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
           - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = ''auto'', one job will be launched for each identified CPU core on the host. [default: 1]'
+              - --p-replicate-handling
+            argument: TEXT Choices('error', 'random', 'drop')
+            description: 'Choose how replicate samples are handled. If replicates are detected, "error" causes method to fail; "drop" will discard all replicated samples; "random" chooses one representative at random from among replicates. [default: ''error'']'
           - names:
-              - --o-distance-matrix
-            argument: ARTIFACT
-            description: Distance matrix for Bray-Curtis dissimilarity
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -4040,34 +8671,51 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-          - names:
-              - --o-distance-matrix
-            argument: bray-curtis-dm.qza
-            description: '# ### example: use ''auto'' to run on all of host system''s available CPU cores'
-      - name: faith-pd
-        description: Faith's Phylogenetic Diversity
-        usage: qiime diversity-lib faith-pd [OPTIONS]
+      - name: pairwise-distances
+        description: Paired pairwise distance testing and boxplots
+        usage: qiime longitudinal pairwise-distances [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable
-            description: The feature table containing the samples for which
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of distances between pairs of samples. [required]
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence
-            description: The feature table containing the samples for which
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata file containing individual-id-column. [required]
           - names:
-              - --i-phylogeny
-            argument: ARTIFACT
-            description: Phylogenetic tree containing tip identifiers that   Phylogeny[Rooted] correspond to the feature identifiers in the table.
+              - --p-group-column
+            argument: TEXT
+            description: Metadata column on which to separate groups for comparison [required]
           - names:
-              - --p-threads
-            argument: NTHREADS
-            description: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.
+              - --p-state-column
+            argument: TEXT
+            description: Metadata column containing state (e.g., Time) across which samples are paired. [required]
           - names:
-              - --o-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector containing per-sample values for Faith's Phylogenetic Diversity. [required]
+              - --p-state-1
+            argument: TEXT
+            description: Baseline state column value. [required]
+          - names:
+              - --p-state-2
+            argument: TEXT
+            description: State column value to pair with baseline. [required]
+          - names:
+              - --p-individual-id-column
+            argument: TEXT
+            description: 'Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling="random" to instead randomly select one member. [required]'
+          - names:
+              - --p-parametric
+              - --p-no-parametric
+            argument: ""
+            description: Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
+          - names:
+              - --p-replicate-handling
+            argument: TEXT Choices('error', 'random', 'drop')
+            description: 'Choose how replicate samples are handled. If replicates are detected, "error" causes method to fail; "drop" will discard all replicated samples; "random" chooses one representative at random from among replicates. [default: ''error'']'
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -4089,26 +8737,50 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: jaccard
-        description: Jaccard Distance
-        usage: qiime diversity-lib jaccard [OPTIONS]
+      - name: plot-feature-volatility
+        description: Plot longitudinal feature volatility and importances
+        usage: qiime longitudinal plot-feature-volatility [OPTIONS]
         options:
           - names:
               - --i-table
-            argument: ARTIFACT FeatureTable
-            description: The feature table containing the samples for which
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: Feature table containing features found in importances. [required]
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence
-            description: The feature table containing the samples for which
+              - --i-importances
+            argument: ARTIFACT FeatureData[Importance]
+            description: Feature importance scores. [required]
           - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n-jobs = ''auto'', one job will be launched for each identified CPU core on the host. [default: 1]'
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata file containing individual-id-column. [required]
           - names:
-              - --o-distance-matrix
-            argument: ARTIFACT
-            description: Distance matrix for Jaccard index [required]
+              - --p-state-column
+            argument: TEXT
+            description: Metadata column containing state (time) variable information. [required]
+          - names:
+              - --p-individual-id-column
+            argument: TEXT
+            description: Metadata column containing IDs for individual subjects. [optional]
+          - names:
+              - --p-default-group-column
+            argument: TEXT
+            description: The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization).
+          - names:
+              - --p-yscale
+            argument: TEXT Choices('linear', 'pow', 'sqrt', 'log')
+            description: 'y-axis scaling strategy to apply. [default: ''linear'']'
+          - names:
+              - --p-importance-threshold
+            argument: VALUE
+            description: Filter feature table to exclude any features with an importance score less than this threshold.
+          - names:
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -4130,26 +8802,42 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-          - names:
-              - --o-distance-matrix
-            argument: jaccard-dm.qza
-            description: '# ### example: use ''auto'' to run on all of host system''s available CPU cores'
-      - name: observed-features
-        description: Observed Features
-        usage: qiime diversity-lib observed-features [OPTIONS]
+      - name: volatility
+        description: Generate interactive volatility plot
+        usage: qiime longitudinal volatility [OPTIONS]
         options:
           - names:
               - --i-table
-            argument: ARTIFACT FeatureTable
-            description: The feature table containing the samples for which the
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: Feature table containing metrics. [optional]
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence
-            description: The feature table containing the samples for which the
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata file containing individual-id-column. [required]
           - names:
-              - --o-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector containing per-sample counts of observed features. [required]
+              - --p-state-column
+            argument: TEXT
+            description: Metadata column containing state (time) variable information. [required]
+          - names:
+              - --p-individual-id-column
+            argument: TEXT
+            description: Metadata column containing IDs for individual subjects. [optional]
+          - names:
+              - --p-default-group-column
+            argument: TEXT
+            description: The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization).
+          - names:
+              - --p-default-metric
+            argument: TEXT
+            description: Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization). [optional]
+          - names:
+              - --p-yscale
+            argument: TEXT Choices('linear', 'pow', 'sqrt', 'log')
+            description: 'y-axis scaling strategy to apply. [default: ''linear'']'
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -4171,23 +8859,40 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: pielou-evenness
-        description: Pielou's Evenness
-        usage: qiime diversity-lib pielou-evenness [OPTIONS]
+  - name: metadata
+    description: Plugin for working with Metadata.
+    usage: qiime metadata [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: distance-matrix
+        description: Create a distance matrix from a numeric Metadata column
+        usage: qiime metadata distance-matrix [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency]
-            description: The feature table containing the samples for which Pielou's evenness should be computed. [required]
-          - names:
-              - --p-drop-undefined-samples
-              - --p-no-drop-undefined-samples
-            argument: ""
-            description: 'Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector. [default: False]'
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Numeric metadata column to compute pairwise Euclidean distances from [required]
           - names:
-              - --o-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector containing per-sample values for Pielou's Evenness. [required]
+              - --o-distance-matrix
+            argument: ARTIFACT
+            description: DistanceMatrix [required]
           - names:
               - --output-dir
             argument: PATH
@@ -4209,23 +8914,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: shannon-entropy
-        description: Shannon's Entropy
-        usage: qiime diversity-lib shannon-entropy [OPTIONS]
+      - name: merge
+        description: Merge metadata
+        usage: qiime metadata merge [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency]
-            description: The feature table containing the samples for which Shannon's Entropy should be computed. [required]
+              - --m-metadata1-file
+            argument: METADATA...
+            description: First metadata file to merge. [required]
           - names:
-              - --p-drop-undefined-samples
-              - --p-no-drop-undefined-samples
-            argument: ""
-            description: 'Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector. [default: False]'
+              - --m-metadata2-file
+            argument: METADATA...
+            description: Second metadata file to merge. [required]
           - names:
-              - --o-vector
-            argument: ARTIFACT SampleData[AlphaDiversity]
-            description: Vector containing per-sample values for Shannon's Entropy. [required]
+              - --o-merged-metadata
+            argument: ARTIFACT
+            description: ImmutableMetadata The merged metadata. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -4247,35 +8951,36 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: unweighted-unifrac
-        description: Unweighted Unifrac
-        usage: qiime diversity-lib unweighted-unifrac [OPTIONS]
-        options:
-          - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable
-            description: The feature table containing the samples for which
+      - name: shuffle-groups
+        description: Shuffle values in a categorical sample metadata column.
+        usage: qiime metadata shuffle-groups [OPTIONS]
+        options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTableFrequency | RelativeFrequency |   PresenceAbsence
-            description: The feature table containing the samples for which
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Categorical metadata column to shuffle. [required]
           - names:
-              - --i-phylogeny
-            argument: ARTIFACT
-            description: Phylogenetic tree containing tip identifiers that   Phylogeny[Rooted] correspond to the feature identifiers in the table.
+              - --p-n-columns
+            argument: INTEGER
+            description: The number of shuffled metadata columns to create.
           - names:
-              - --p-threads
-            argument: NTHREADS
-            description: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.
+              - --p-md-column-name-prefix
+            argument: TEXT
+            description: 'Prefix to use in naming the shuffled metadata columns. [default: ''shuffled.grouping.'']'
           - names:
-              - --p-bypass-tips
-              - --p-no-bypass-tips
+              - --p-md-column-values-prefix
+            argument: TEXT
+            description: 'Prefix to use in naming the values in the shuffled metadata columns. [default: ''fake.group.'']'
+          - names:
+              - --p-encode-sample-size
+              - --p-no-encode-sample-size
             argument: ""
-            description: 'In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]'
+            description: If true, the sample size of each metadata group will be appended to the shuffled metadata column values.
           - names:
-              - --o-distance-matrix
-            argument: ARTIFACT
-            description: Distance matrix for Unweighted Unifrac. [required]
+              - --o-shuffled-groups
+            argument: ARTIFACT SampleData[ArtificialGrouping]
+            description: Randomized metadata columns [required]
           - names:
               - --output-dir
             argument: PATH
@@ -4297,35 +9002,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-          - names:
-              - --o-distance-matrix
-            argument: unweighted-unifrac-dm.qza
-            description: '# ### example: to run on n cores, replace 1 here with your preferred integer'
-      - name: weighted-unifrac
-        description: Weighted Unifrac
-        usage: qiime diversity-lib weighted-unifrac [OPTIONS]
+      - name: tabulate
+        description: Interactively explore Metadata in an HTML table
+        usage: qiime metadata tabulate [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency]
-            description: The feature table containing the samples for which Weighted Unifrac should be computed. [required]
-          - names:
-              - --i-phylogeny
-            argument: ARTIFACT
-            description: Phylogenetic tree containing tip identifiers that
-          - names:
-              - --p-threads
-            argument: NTHREADS
-            description: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.
+            - --m-input-file
+            argument: METADATA...
+            description: The metadata to tabulate. [required]
           - names:
-              - --p-bypass-tips
-              - --p-no-bypass-tips
-            argument: ""
-            description: 'In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]'
+              - --p-page-size
+            argument: INTEGER
+            description: 'The maximum number of Metadata records to display per page [default: 100]'
           - names:
-              - --o-distance-matrix
-            argument: ARTIFACT
-            description: Distance matrix for Unweighted Unifrac. [required]
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -4347,13 +9039,9 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-          - names:
-              - --o-distance-matrix
-            argument: weighted-unifrac-dm.qza
-            description: '# ### example: to run on n cores, replace 1 here with your preferred integer'
-  - name: emperor
-    description: Plugin for ordination plotting with Emperor.
-    usage: qiime emperor [OPTIONS] COMMAND [ARGS]...
+  - name: moshpit
+    description: QIIME 2 plugin for metagenome analysis.
+    usage: qiime moshpit [OPTIONS] COMMAND [ARGS]...
     options:
       - names:
           - --version
@@ -4367,45 +9055,90 @@ subcommands:
           - --citations
         argument: ""
         description: Show citations and exit.
+      - names:
+          - --show-hidden-actions
+        argument: ""
+        description: This plugin has hidden actions with names starting with '_'. These are generally called internally by pipelines. Passing this flag will display those actions.
       - names:
           - --help
         argument: ""
         description: Show this message and exit.
     subcommands:
-      - name: biplot
-        description: Visualize and Interact with Principal Coordinates Analysis
-        usage: qiime emperor biplot [OPTIONS]
+      - name: bin-contigs-metabat
+        description: Bin contigs into MAGs using MetaBAT 2.
+        usage: qiime moshpit bin-contigs-metabat [OPTIONS]
         options:
           - names:
-              - --i-biplot
+              - --i-contigs
             argument: ARTIFACT
-            description: The principal coordinates matrix to be plotted. [required]
+            description: Contigs to be binned. [required]
           - names:
-              - --m-sample-metadata-file
-            argument: METADATA...
-            description: The sample metadata [required]
+              - --i-alignment-maps
+            argument: ARTIFACT
+            description: Reads-to-contig alignment maps. [required]
           - names:
-              - --m-feature-metadata-file
-            argument: METADATA...
-            description: The feature metadata (useful to manipulate the arrows in the plot).
+              - --p-min-contig
+            argument: INTEGER
+            description: Minimum size of a contig for binning.
           - names:
-              - --p-ignore-missing-samples
-              - --p-no-ignore-missing-samples
+              - --p-max-p
+            argument: INTEGER
+            description: Percentage of "good" contigs considered for binning decided by connection among contigs.
+          - names:
+              - --p-min-s
+            argument: INTEGER
+            description: Minimum score of a edge for binning.
+          - names:
+              - --p-max-edges
+            argument: INTEGER
+            description: Maximum number of edges per node.
+          - names:
+              - --p-p-tnf
+            argument: INTEGER
+            description: TNF probability cutoff for building TNF graph.
+          - names:
+              - --p-no-add
+              - --p-no-no-add
             argument: ""
-            description: 'This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]'
+            description: Turning off additional binning for lost or small contigs.
           - names:
-              - --p-invert
-              - --p-no-invert
+              - --p-min-cv
+            argument: INTEGER
+            description: Minimum mean coverage of a contig in each library for binning.
+          - names:
+              - --p-min-cv-sum
+            argument: INTEGER
+            description: Minimum total effective mean coverage of a contig (sum of depth over minCV) for binning.
+          - names:
+              - --p-min-cls-size
+            argument: INTEGER
+            description: Minimum size of a bin as the output. [optional]
+          - names:
+              - --p-seed
+            argument: INTEGER
+            description: 'For exact reproducibility. (0: use random seed)'
+          - names:
+              - --p-debug
+              - --p-no-debug
             argument: ""
-            description: 'If specified, the point and arrow coordinates will be swapped. [default: False]'
+            description: Debug output. [optional]
           - names:
-              - --p-number-of-features
+              - --p-verbose
+              - --p-no-verbose
             argument: ""
-            description: INTEGER
+            description: Verbose output. [optional]
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-mags
+            argument: ARTIFACT
+            description: The resulting MAGs. [required]
+          - names:
+              - --o-contig-map
+            argument: ARTIFACT
+            description: Mapping of MAG identifiers to the contig identifiers contained in each MAG. [required]
+          - names:
+              - --o-unbinned-contigs
+            argument: ARTIFACT
+            description: Contigs that were not binned into any MAG. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -4427,36 +9160,40 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: plot
-        description: Visualize and Interact with Principal Coordinates Analysis
-        usage: qiime emperor plot [OPTIONS]
+      - name: build-custom-diamond-db
+        description: Create a DIAMOND formatted reference database from a FASTA input file.
+        usage: qiime moshpit build-custom-diamond-db [OPTIONS]
         options:
           - names:
-              - --i-pcoa
+              - --i-seqs
             argument: ARTIFACT
-            description: The principal coordinates matrix to be plotted. [required]
+            description: Protein reference database. [required]
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata. [required]
+              - --i-taxonomy
+            argument: ARTIFACT
+            description: Reference taxonomy, needed to provide taxonomy features. [optional]
           - names:
-              - --p-ignore-missing-samples
-              - --p-no-ignore-missing-samples
+              - --p-threads
+            argument: INTEGER
+            description: Number of CPU threads.
+          - names:
+              - --p-ignore-warnings
+              - --p-no-ignore-warnings
             argument: ""
-            description: 'This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]'
+            description: 'Ignore warnings. [default: False]'
           - names:
-              - --p-ignore-pcoa-features
-              - --p-no-ignore-pcoa-features
+              - --p-no-parse-seqids
+              - --p-no-no-parse-seqids
             argument: ""
-            description: 'Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the `biplot` method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised. [default: False]'
+            description: 'Print raw seqids without parsing. [default: False]'
           - names:
-              - --p-custom-axes
-            argument: TEXT...
-            description: Numeric sample metadata columns that should be included as axes in the Emperor plot.
+              - --p-file-buffer-size
+            argument: INTEGER
+            description: 'Range(1, None) File buffer size in bytes. [default: 67108864]'
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-diamond-db
+            argument: ARTIFACT
+            description: DIAMOND database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -4478,39 +9215,106 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: procrustes-plot
-        description: Visualize and Interact with a procrustes plot
-        usage: qiime emperor procrustes-plot [OPTIONS]
+      - name: build-eggnog-diamond-db
+        description: Create a DIAMOND formatted reference database for the specified taxon.
+        usage: qiime moshpit build-eggnog-diamond-db [OPTIONS]
         options:
           - names:
-              - --i-reference-pcoa
+              - --i-eggnog-proteins
             argument: ARTIFACT
-            description: The reference ordination matrix to be plotted. [required]
+            description: eggNOG database of protein sequences and their corresponding taxonomy information (generated through the `fetch-eggnog-proteins` action). [required]
           - names:
-              - --i-other-pcoa
+              - --p-taxon
+            argument: INTEGER
+            description: Taxon ID number. [required]
+          - names:
+              - --o-diamond-db
             argument: ARTIFACT
-            description: The "other" ordination matrix to be plotted (the one that was fitted to the reference). [required]
+            description: Complete Diamond reference database for thespecified taxon. [required]
           - names:
-              - --i-m2-stats
-            argument: ARTIFACT ProcrustesStatistics
-            description: The M^2 value of the procrustes analysis & its associated p value. [optional]
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata. [required]
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-custom-axes
-            argument: TEXT...
-            description: Numeric sample metadata columns that should be included as axes in the Emperor plot.
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-ignore-missing-samples
-              - --p-no-ignore-missing-samples
+              - --citations
             argument: ""
-            description: 'This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]'
+            description: Show citations and exit.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: build-kraken-db
+        description: Build Kraken 2 database.
+        usage: qiime moshpit build-kraken-db [OPTIONS]
+        options:
+          - names:
+              - --i-seqs
+            argument: ARTIFACTS...
+            description: Sequences to be added to the Kraken 2 database.
+          - names:
+              - --p-collection
+            argument: '{viral, minusb, standard, standard8, standard16, pluspf, pluspf8, pluspf16, pluspfp, pluspfp8, pluspfp16, eupathdb, nt, greengenes, rdp, silva132, silva138}'
+            description: Name of the database collection to be fetched.
+          - names:
+              - --p-threads
+            argument: INTEGER
+            description: 'Number of threads. Only applicable when building a custom database. [default: 1]'
+          - names:
+              - --p-kmer-len
+            argument: INTEGER
+            description: 'K-mer length in bp/aa. [default: 35]'
+          - names:
+              - --p-minimizer-len
+            argument: INTEGER
+            description: 'Minimizer length in bp/aa. [default: 31]'
+          - names:
+              - --p-minimizer-spaces
+            argument: INTEGER
+            description: Number of characters in minimizer that are ignored
+          - names:
+              - --p-max-db-size
+            argument: INTEGER
+            description: Maximum number of bytes for Kraken 2 hash table
+          - names:
+              - --p-load-factor
+            argument: PROPORTION
+            description: Proportion of the hash table to be populated.
+          - names:
+              - --p-read-len
+            argument: INTEGERS...
+            description: Ideal read lengths to be used while building the Bracken database.
+          - names:
+              - --p-no-masking
+              - --p-no-no-masking
+            argument: ""
+            description: 'Avoid masking low-complexity sequences prior to building; masking requires dustmasker or segmasker to be installed in PATH [default: False]'
+          - names:
+              - --p-use-ftp
+              - --p-no-use-ftp
+            argument: ""
+            description: Use FTP for downloading instead of RSYNC.
+          - names:
+              - --p-fast-build
+              - --p-no-fast-build
+            argument: ""
+            description: 'Do not require database to be deterministically built when using multiple threads. This is faster, but does introduce variability in minimizer/LCA pairs. [default: False]'
+          - names:
+              - --o-kraken2-database
+            argument: ARTIFACT
+            description: Kraken2DB Kraken2 database. [required]
+          - names:
+              - --o-bracken-database
+            argument: ARTIFACT
+            description: BrackenDB Bracken database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -4530,78 +9334,75 @@ subcommands:
             description: Show citations and exit.
           - names:
               - --help
-            argument: ""
-            description: Show this message and exit.
-  - name: feature-classifier
-    description: Plugin for taxonomic classification.
-    usage: qiime feature-classifier [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: blast
-        description: BLAST+ local alignment search.
-        usage: qiime feature-classifier blast [OPTIONS]
+            argument: ""
+            description: Show this message and exit.
+      - name: classify-kaiju
+        description: Classify reads using Kaiju.
+        usage: qiime moshpit classify-kaiju [OPTIONS]
         options:
           - names:
-              - --i-query
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Query sequences. [required]
-          - names:
-              - --i-reference-reads
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequences. Incompatible with blastdb.
+            - --i-seqs
+            argument: ARTIFACT
+            description: Sequences to be classified. [required]
           - names:
-              - --i-blastdb
+              - --i-db
             argument: ARTIFACT
-            description: BLAST indexed database. Incompatible with
+            description: Kaiju database. [required]
           - names:
-              - --p-maxaccepts
+              - --p-z
             argument: INTEGER
-            description: Maximum number of hits to keep for each query.
+            description: Number of threads.
           - names:
-              - --p-perc-identity
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: Reject match if percent identity to query is lower.
+              - --p-a
+            argument: TEXT Choices('greedy', 'mem')
+            description: 'Run mode. [default: ''greedy'']'
           - names:
-              - --p-query-cov
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: 'Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn''s qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. [default: 0.8]'
+              - --p-e
+            argument: INTEGER
+            description: Number of mismatches allowed in Greedy mode.
           - names:
-              - --p-strand
-            argument: TEXT Choices('both', 'plus', 'minus')
-            description: 'Align against reference sequences in forward ("plus"), reverse ("minus"), or both directions ("both"). [default: ''both'']'
+              - --p-m
+            argument: INTEGER
+            description: Minimum match length.
+          - names:
+              - --p-s
+            argument: INTEGER
+            description: Minimum match score in Greedy mode.
           - names:
               - --p-evalue
+            argument: PROPORTION
+            description: Minimum E-value in Greedy mode.
+          - names:
+              - --p-x
+              - --p-no-x
+            argument: ""
+            description: 'Enable SEG low complexity filter. [default: True]'
+          - names:
+              - --p-r
+            argument: TEXT Choices('phylum', 'class', 'order', 'family', 'genus', 'species')
+            description: Taxonomic rank.
+          - names:
+              - --p-c
             argument: NUMBER
-            description: 'BLAST expectation value (E) threshold for saving hits. [default: 0.001]'
+            description: Minimum required number or fraction of reads for the taxon  (except viruses) to be reported.
           - names:
-              - --p-output-no-hits
-              - --p-no-output-no-hits
+              - --p-exp
+              - --p-no-exp
             argument: ""
-            description: 'Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. Set to FALSE to mirror default BLAST search.'
+            description: Expand viruses, which are always shown as full taxon
           - names:
-              - --p-num-threads
-            argument: NTHREADS
-            description: Number of threads (CPUs) to use in the BLAST search. Pass 0 to use all available CPUs.
+              - --p-u
+              - --p-no-u
+            argument: ""
+            description: Do not count unclassified reads for the total reads
           - names:
-              - --o-search-results
-            argument: ARTIFACT
-            description: FeatureData[BLAST6] Top hits for each query. [required]
+              - --o-abundances
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Read abundances. [required]
+          - names:
+              - --o-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Linked taxonomy. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -4623,71 +9424,61 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: classify-consensus-blast
-        description: BLAST+ consensus taxonomy classifier
-        usage: qiime feature-classifier classify-consensus-blast [OPTIONS]
+      - name: classify-kraken2
+        description: Perform taxonomic classification of reads or MAGs using Kraken 2.
+        usage: qiime moshpit classify-kraken2 [OPTIONS]
         options:
           - names:
-              - --i-query
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Query sequences. [required]
-          - names:
-              - --i-reference-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: reference taxonomy labels. [required]
-          - names:
-              - --i-blastdb
+            - --i-seqs
             argument: ARTIFACT
-            description: BLAST indexed database. Incompatible with
+            description: Sequences to be classified. [required]
           - names:
-              - --i-reference-reads
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequences. Incompatible with blastdb.
+              - --i-kraken2-db
+            argument: ARTIFACT Kraken 2 database.
+            description: Kraken2DB [required]
           - names:
-              - --p-maxaccepts
+              - --p-threads
             argument: INTEGER
-            description: Maximum number of hits to keep for each query.
-          - names:
-              - --p-perc-identity
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: Reject match if percent identity to query is lower.
+            description: Number of threads.
           - names:
-              - --p-query-cov
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: 'Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn''s qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. [default: 0.8]'
+              - --p-confidence
+            argument: PROPORTION
+            description: 'Confidence score threshold. [default: 0.0]'
           - names:
-              - --p-strand
-            argument: TEXT Choices('both', 'plus', 'minus')
-            description: 'Align against reference sequences in forward ("plus"), reverse ("minus"), or both directions ("both"). [default: ''both'']'
+              - --p-minimum-base-quality
+            argument: INTEGER
+            description: Minimum base quality used in classification.
           - names:
-              - --p-evalue
-            argument: NUMBER
-            description: 'BLAST expectation value (E) threshold for saving hits. [default: 0.001]'
+              - --p-memory-mapping
+              - --p-no-memory-mapping
+            argument: ""
+            description: Avoids loading the database into RAM.
           - names:
-              - --p-output-no-hits
-              - --p-no-output-no-hits
+              - --p-quick
+              - --p-no-quick
             argument: ""
-            description: 'Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. Set to FALSE to mirror default BLAST search.'
+            description: Quick operation (use first hit or hits).
           - names:
-              - --p-min-consensus
-            argument: NUMBER
-            description: Minimum fraction of assignments must match top hit to be accepted as consensus assignment.
+              - --p-report-minimizer-data
+              - --p-no-report-minimizer-data
+            argument: ""
+            description: Include number of read-minimizers per-taxon and unique read-minimizers per-taxon in the repot.
           - names:
-              - --p-unassignable-label
-            argument: TEXT
-            description: Annotation given to sequences without any hits.
+              - --p-minimum-hit-groups
+            argument: INTEGER
+            description: Minimum number of hit groups (overlapping k-mers sharing the same minimizer).
           - names:
-              - --p-num-threads
-            argument: NTHREADS
-            description: Number of threads (CPUs) to use in the BLAST search. Pass 0 to use all available CPUs.
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the contigs into.
           - names:
-              - --o-classification
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomy classifications of query sequences.
+              - --o-reports
+            argument: ARTIFACT
+            description: Reports produced by Kraken2. [required]
           - names:
-              - --o-search-results
+              - --o-hits
             argument: ARTIFACT
-            description: FeatureData[BLAST6] Top hits for each query. [required]
+            description: Output files produced by Kraken2. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -4729,85 +9520,183 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: classify-consensus-vsearch
-        description: VSEARCH-based consensus taxonomy classifier
-        usage: "qiime feature-classifier classify-consensus-vsearch [OPTIONS]"
+      - name: collate-annotations
+        description: Collate ortholog annotations.
+        usage: qiime moshpit collate-annotations [OPTIONS]
         options:
           - names:
-              - --i-query
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Query Sequences. [required]
+              - --i-ortholog-annotations
+            argument: ARTIFACTS...
+            description: Collection of ortholog annotations. [required]
           - names:
-              - --i-reference-reads
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequences. [required]
+              - --o-collated-annotations
+            argument: ARTIFACT
+            description: FeatureData[NOG] Collated ortholog annotations. [required]
           - names:
-              - --i-reference-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Reference taxonomy labels. [required]
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-maxaccepts
-            argument: VALUE
-            description: Maximum number of hits to keep for each query.
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-perc-identity
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: Reject match if percent identity to query is lower.
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-query-cov
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: 'Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8]'
+              - --citations
+            argument: ""
+            description: Show citations and exit.
           - names:
-              - --p-strand
-            argument: TEXT Choices('both', 'plus')
-            description: Align against reference sequences in forward ("plus") or both directions ("both").
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: collate-busco-results
+        description: Collate BUSCO results.
+        usage: qiime moshpit collate-busco-results [OPTIONS]
+        options:
           - names:
-              - --p-search-exact
-              - --p-no-search-exact
+              - --i-busco-results
+            argument: ARTIFACTS...
+            description: '[required]'
+          - names:
+              - --o-collated-busco-results
+            argument: ARTIFACT
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
             argument: ""
-            description: 'Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity, query-cov, maxaccepts, and maxrejects settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False]'
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-top-hits-only
-              - --p-no-top-hits-only
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
             argument: ""
-            description: 'Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False]'
+            description: Show citations and exit.
           - names:
-              - --p-maxhits
-            argument: VALUE
-            description: Maximum number of hits to show once the search is terminated.
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: collate-feature-data-mags
+        description: Collate mags
+        usage: qiime moshpit collate-feature-data-mags [OPTIONS]
+        options:
           - names:
-              - --p-maxrejects
-            argument: VALUE
-            description: Maximum number of non-matching target sequences to consider before stopping the search.
+              - --i-mags
+            argument: ARTIFACTS...
+            description: A collection of MAGs to be collated. [required]
           - names:
-              - --p-output-no-hits
-              - --p-no-output-no-hits
+              - --o-collated-mags
+            argument: ARTIFACT
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
             argument: ""
-            description: 'Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs.'
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-weak-id
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: 'Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0]'
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-threads
-            argument: NTHREADS
-            description: 'Number of threads to use for job parallelization. Pass 0 to use one per available CPU. [default: 1]'
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: collate-kraken2-outputs
+        description: Collate kraken2 outputs
+        usage: qiime moshpit collate-kraken2-outputs [OPTIONS]
+        options:
+          - names:
+              - --i-kraken2-outputs
+            argument: ARTIFACTS...
+            description: '[required]'
+          - names:
+              - --o-collated-kraken2-outputs
+            argument: ARTIFACTS...
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: collate-kraken2-reports
+        description: Collate kraken2 reports
+        usage: qiime moshpit collate-kraken2-reports [OPTIONS]
+        options:
+          - names:
+              - --i-kraken2-reports
+            argument: ARTIFACTS...
+            description: '[required]'
+          - names:
+              - --o-collated-kraken2-reports
+            argument: ARTIFACTS...
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-min-consensus
-            argument: NUMBER
-            description: Minimum fraction of assignments must match top hit to be accepted as consensus assignment.
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-unassignable-label
-            argument: TEXT
-            description: Annotation given to sequences without any hits.
+              - --citations
+            argument: ""
+            description: Show citations and exit.
           - names:
-              - --o-classification
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomy classifications of query sequences. [required]
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: collate-orthologs
+        description: Collate Orthologs
+        usage: qiime moshpit collate-orthologs [OPTIONS]
+        options:
           - names:
-              - --o-search-results
+              - --i-orthologs
+            argument: ARTIFACTS...
+            description: Orthologs to collate [required]
+          - names:
+              - --o-collated-orthologs
             argument: ARTIFACT
-            description: FeatureData[BLAST6] Top hits for each query. [required]
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -4818,25 +9707,38 @@ subcommands:
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --no-recycle
+              - --citations
             argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+            description: Show citations and exit.
           - names:
-              - --parallel
+              - --help
             argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
+            description: Show this message and exit.
+      - name: collate-sample-data-mags
+        description: Collate mags
+        usage: qiime moshpit collate-sample-data-mags [OPTIONS]
+        options:
           - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
+              - --i-mags
+            argument: ARTIFACTS...
+            description: A collection of MAGs to be collated. [required]
           - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+              - --o-collated-mags
+            argument: ARTIFACT
+            description: SampleData[MAGs] [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
               - --example-data
             argument: PATH
@@ -4849,87 +9751,80 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: classify-hybrid-vsearch-sklearn
-        description: 'ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier'
-        usage: qiime feature-classifier classify-hybrid-vsearch-sklearn
+      - name: dereplicate-mags
+        description: Dereplicate MAGs from multiple samples.
+        usage: qiime moshpit dereplicate-mags [OPTIONS]
         options:
           - names:
-              - --i-query
-            argument: ARTIFACT
-            description: Query Sequences. [required]
-          - names:
-              - --i-reference-reads
-            argument: ARTIFACT
-            description: Reference sequences. [required]
-          - names:
-              - --i-reference-taxonomy
+              - --i-mags
             argument: ARTIFACT
-            description: Reference taxonomy labels. [required]
+            description: MAGs to be dereplicated. [required]
           - names:
-              - --i-classifier
+              - --i-distance-matrix
             argument: ARTIFACT
-            description: Pre-trained sklearn taxonomic classifier for classifying the reads. [required]
-          - names:
-              - --p-maxaccepts
-            argument: VALUE
-            description: 'Maximum number of hits to keep for each query. Set to "all" to keep all hits > perc-identity similarity. Note that if strand=both, maxaccepts will keep N hits for each direction (if searches in the opposite direction yield results that exceed the minimum perc-identity). In those cases use maxhits to control the total number of hits returned. This option works in pair with maxrejects. The search process sorts target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if the first target sequence passes the acceptation criteria, it is accepted as best hit and the search process stops for that query. If maxaccepts is set to a higher value, more hits are accepted. If maxaccepts and maxrejects are both set to "all", the complete database is searched. [default: 10]'
+            description: Matrix of distances between MAGs. [required]
           - names:
-              - --p-perc-identity
+              - --p-threshold
             argument: PROPORTION
-            description: 'Percent sequence similarity to use for PREFILTER. Reject match if percent identity to query is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.5]'
+            description: 'Similarity threshold required to consider two bins identical. [default: 0.99]'
           - names:
-              - --p-query-cov
-            argument: PROPORTION
-            description: 'Query coverage threshold to use for PREFILTER. Reject match if query alignment coverage per high-scoring pair is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.8]'
+              - --o-dereplicated-mags
+            argument: ARTIFACT
+            description: Dereplicated MAGs. [required]
           - names:
-              - --p-strand
-            argument: '{''both'', ''plus''}'
-            description: 'Align against reference sequences in forward ("plus") or both directions ("both"). [default: ''both'']'
+              - --o-feature-table
+            argument: ARTIFACT
+            description: Mapping between MAGs and samples. [required]
           - names:
-              - --p-min-consensus
-            argument: NUMBER
-            description: Minimum fraction of assignments must match top hit to be accepted as consensus assignment.
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-maxhits
-            argument: VALUE
-            description: 'max hits [default: ''all'']'
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-maxrejects
-            argument: VALUE
-            description: 'max rejects [default: ''all'']'
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-reads-per-batch
-            argument: VALUE
-            description: 'Number of reads to process in each batch for sklearn classification. If "auto", this parameter is autoscaled to min(number of query sequences / threads, 20000). [default: ''auto'']'
+              - --citations
+            argument: ""
+            description: Show citations and exit.
           - names:
-              - --p-confidence
-            argument: VALUE Float
-            description: Confidence threshold for limiting taxonomic depth. Set to "disable" to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments.
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: eggnog-annotate
+        description: Annotate orthologs against eggNOG database
+        usage: qiime moshpit eggnog-annotate [OPTIONS]
+        options:
           - names:
-              - --p-read-orientation
-            argument: '{''same'', ''reverse-complement'', ''auto''}'
-            description: 'Direction of reads with respect to reference sequences in pre-trained sklearn classifier. same will cause reads to be classified unchanged; reverse-complement will cause reads to be reversed and complemented prior to classification. "auto" will autodetect orientation based on the confidence estimates for the first 100 reads. [default: ''auto'']'
+              - --i-eggnog-hits
+            argument: ARTIFACT
+            description: SampleData[BLAST6] BLAST6-like table(s) describing the identified orthologs. [required]
           - names:
-              - --p-threads
-            argument: INTEGER
-            description: 'Number of threads to use for job parallelization. [default: 1]'
+              - --i-eggnog-db
+            argument: ARTIFACT
+            description: eggNOG annotation database. [required]
           - names:
-              - --p-prefilter
-              - --p-no-prefilter
+              - --p-db-in-memory
+              - --p-no-db-in-memory
             argument: ""
-            description: 'Toggle positive filter of query sequences on or off. [default: True]'
+            description: 'Read eggnog database into memory. The eggnog database is very large(>44GB), so this option should only be used on clusters or other machines with enough memory. [default: False]'
           - names:
-              - --p-sample-size
+              - --p-num-cpus
             argument: INTEGER
-            description: 'Randomly extract the given number of sequences from the reference database to use for prefiltering. This parameter is ignored if `prefilter` is disabled. [default: 1000]'
+            description: Number of CPUs to utilize. '0' will use all available.
           - names:
-              - --p-randseed
+              - --p-num-partitions
             argument: INTEGER
-            description: Use integer as a seed for the pseudo-random
+            description: Range(1, None) The number of partitions to split the contigs into.
           - names:
-              - --o-classification
+              - --o-ortholog-annotations
             argument: ARTIFACT
-            description: Taxonomy classifications of query sequences. [required]
+            description: Annotated hits. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -4971,33 +9866,38 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: classify-sklearn
-        description: Pre-fitted sklearn-based taxonomy classifier
-        usage: qiime feature-classifier classify-sklearn [OPTIONS]
+      - name: eggnog-diamond-search
+        description: Run eggNOG search using diamond aligner
+        usage: qiime moshpit eggnog-diamond-search [OPTIONS]
         options:
           - names:
-              - --i-reads
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The feature data to be classified. [required]
+              - --i-sequences
+            argument: ARTIFACT
+            description: Sequence data of the contigs we want to search for hits using the Diamond Database [required]
           - names:
-              - --i-classifier
+              - --i-diamond-db
             argument: ARTIFACT
-            description: TaxonomicClassifier The taxonomic classifier for classifying the reads.
+            description: The filepath to an artifact containing the Diamond database [required]
           - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]'
+              - --p-num-cpus
+            argument: INTEGER
+            description: 'Number of CPUs to utilize. ''0'' will use all available. [default: 1]'
           - names:
-              - --p-pre-dispatch
-            argument: TEXT
-            description: '"all" or expression, as in "3*n_jobs". The number of batches (of tasks) to be pre-dispatched.'
+              - --p-db-in-memory
+              - --p-no-db-in-memory
+            argument: ""
+            description: Read database into memory. The database can be very large, so this option should only be used on clusters or other machines with enough memory.
           - names:
-              - --p-read-orientation
-            argument: TEXT Choices('same', 'reverse-complement', 'auto')
-            description: Direction of reads with respect to reference sequences. same will cause reads to be classified unchanged; reverse-complement will cause reads to be reversed and complemented prior to classification. "auto" will autodetect orientation based on the confidence estimates for the first 100 reads.
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the contigs into.
           - names:
-              - --o-classification
-            argument: ARTIFACT FeatureData[Taxonomy]
+              - --o-table
+            argument: ARTIFACT
+            description: '[required]'
+          - names:
+              - --o-eggnog-hits
+            argument: ARTIFACT
             description: '[required]'
           - names:
               - --output-dir
@@ -5009,78 +9909,25 @@ subcommands:
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
           - names:
-              - --citations
+              - --no-recycle
             argument: ""
-            description: Show citations and exit.
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
           - names:
-              - --help
+              - --parallel
             argument: ""
-            description: Show this message and exit.
-      - name: extract-reads
-        description: Extract reads from reference sequences.
-        usage: qiime feature-classifier extract-reads [OPTIONS]
-        options:
-          - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: '[required]'
-          - names:
-              - --p-f-primer
-            argument: TEXT
-            description: forward primer sequence (5' -> 3'). [required]
-          - names:
-              - --p-r-primer
-            argument: TEXT
-            description: reverse primer sequence (5' -> 3'). Do not use reverse-complemented primer sequence. [required]
-          - names:
-              - --p-trim-right
-            argument: INTEGER
-            description: 'trim-right nucleotides are removed from the 3'' end if trim-right is positive. Applied before trunc-len and trim-left. [default: 0]'
-          - names:
-              - --p-trunc-len
-            argument: INTEGER
-            description: read is cut to trunc-len if trunc-len is positive. Applied after trim-right but before trim-left.
-          - names:
-              - --p-trim-left
-            argument: INTEGER
-            description: 'trim-left nucleotides are removed from the 5'' end if trim-left is positive. Applied after trim-right and trunc-len. [default: 0]'
-          - names:
-              - --p-identity
-            argument: NUMBER
-            description: minimum combined primer match identity threshold.
-          - names:
-              - --p-min-length
-            argument: INTEGER
-            description: Minimum amplicon length. Shorter amplicons are
-          - names:
-              - --p-max-length
-            argument: INTEGER
-            description: Maximum amplicon length. Longer amplicons are
-          - names:
-              - --p-n-jobs
-            argument: INTEGER
-            description: Number of seperate processes to run.
-          - names:
-              - --p-read-orientation
-            argument: TEXT Choices('both', 'forward', 'reverse')
-            description: 'Orientation of primers relative to the sequences: "forward" searches for primer hits in the forward direction, "reverse" searches reverse-complement, and "both" searches both directions.'
-          - names:
-              - --o-reads
-            argument: ARTIFACT FeatureData[Sequence]
-            description: '[required]'
+            description: Execute your action in parallel. This flag will use your default parallel config.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -5093,26 +9940,42 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: find-consensus-annotation
-        description: Find consensus among multiple annotations.
-        usage: qiime feature-classifier find-consensus-annotation [OPTIONS]
+      - name: estimate-bracken
+        description: Perform read abundance re-estimation using Bracken.
+        usage: qiime moshpit estimate-bracken [OPTIONS]
         options:
           - names:
-              - --i-search-results
-            argument: ARTIFACT FeatureData[BLAST6]
-            description: Search results in BLAST6 output format [required]
+              - --i-kraken-reports
+            argument: ARTIFACT SampleData
+            description: Reports produced by Kraken2. [required]
+          - names:
+              - --i-bracken-db
+            argument: ARTIFACT
+            description: BrackenDB Bracken database. [required]
+          - names:
+              - --p-threshold
+            argument: INTEGER
+            description: 'Bracken: number of reads required PRIOR to abundance estimation to perform re-estimation.'
+          - names:
+              - --p-read-len
+            argument: INTEGER
+            description: 'Bracken: read length to get all classifications for.'
           - names:
-              - --i-reference-taxonomy
+              - --p-level
+            argument: TEXT Choices('D', 'P', 'C', 'O', 'F', 'G', 'S')
+            description: 'Bracken: taxonomic level to estimate abundance at.'
+          - names:
+              - --o-taxonomy
             argument: ARTIFACT FeatureData[Taxonomy]
-            description: reference taxonomy labels. [required]
+            description: '[required]'
           - names:
-              - --p-unassignable-label
-            argument: TEXT
-            description: Annotation given when no consensus is found.
+              - --o-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: '[required]'
           - names:
-              - --o-consensus-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Consensus taxonomy and scores. [required]
+              - --o-reports
+            argument: ARTIFACT SampleData[Kraken2Report % Properties('bracken')]
+            description: Reports modified by Bracken. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5134,111 +9997,110 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: fit-classifier-naive-bayes
-        description: Train the naive_bayes classifier
-        usage: "qiime feature-classifier fit-classifier-naive-bayes \n    [OPTIONS]"
+      - name: evaluate-busco
+        description: Evaluate quality of the generated MAGs using BUSCO.
+        usage: qiime moshpit evaluate-busco [OPTIONS]
         options:
           - names:
-              - --i-reference-reads
-            argument: ARTIFACT FeatureData[Sequence]
-            description: '[required]'
+              - --i-bins
+            argument: ARTIFACT
+            description: MAGs to be analyzed. [required]
           - names:
-              - --i-reference-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: '[required]'
+              - --p-mode
+            argument: TEXT
+            description: Specify which BUSCO analysis mode to run.
           - names:
-              - --i-class-weight
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: '[optional]'
+              - --p-lineage-dataset
+            argument: TEXT
+            description: Specify the name of the BUSCO lineage to be used. To see all possible options run `busco --list-datasets`. [optional]
           - names:
-              - --p-classify--alpha
-            argument: NUMBER
-            description: '[default: 0.001]'
+              - --p-augustus
+              - --p-no-augustus
+            argument: ""
+            description: Use augustus gene predictor for eukaryote runs.
           - names:
-              - --p-classify--chunk-size
-            argument: INTEGER
-            description: '[default: 20000]'
+              - --p-augustus-parameters
+            argument: TEXT
+            description: 'Pass additional arguments to Augustus. All arguments should be contained within a single string with no white space, with each argument separated by a comma. Example: ''--PARAM1=VALUE1,--PARAM2=VALUE2''.'
           - names:
-              - --p-classify--fit-prior
-              - --p-no-classify--fit-prior
-            argument: ""
-            description: '[default: False]'
+              - --p-augustus-species
+            argument: TEXT
+            description: Specify a species for Augustus training. [optional]
           - names:
-              - --p-feat-ext--alternate-sign
-              - --p-no-feat-ext--alternate-sign
+              - --p-auto-lineage
+              - --p-no-auto-lineage
             argument: ""
-            description: '[default: False]'
+            description: Run auto-lineage to find optimum lineage path.
           - names:
-              - --p-feat-ext--binary
-              - --p-no-feat-ext--binary
+              - --p-auto-lineage-euk
+              - --p-no-auto-lineage-euk
             argument: ""
-            description: '[default: False]'
+            description: 'Run auto-placement just on eukaryote tree to find optimum lineage path. [default: False]'
           - names:
-              - --p-verbose
-              - --p-no-verbose
+              - --p-auto-lineage-prok
+              - --p-no-auto-lineage-prok
             argument: ""
-            description: '[default: False]'
+            description: 'Run auto-lineage just on non-eukaryote trees to find optimum lineage path. [default: False]'
           - names:
-              - --p-classify--class-prior
-            argument: TEXT
-            description: '[default: ''null'']'
+              - --p-cpu
+            argument: INTEGER
+            description: Specify the number (N=integer) of threads/cores to use.
           - names:
-              - --p-feat-ext--analyzer
+              - --p-config
             argument: TEXT
-            description: '[default: ''char_wb'']'
+            description: Provide a config file. [optional]
           - names:
-              - --p-feat-ext--preprocessor
-            argument: TEXT
-            description: '[default: ''null'']'
+              - --p-contig-break
+            argument: INTEGER
+            description: Number of contiguous Ns to signify a break between contigs.
           - names:
-              - --p-feat-ext--stop-words
-            argument: TEXT
-            description: '[default: ''null'']'
+              - --p-evalue
+            argument: NUMBER
+            description: 'E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03, Default: 1e-03. [default: 0.001]'
           - names:
-              - --p-feat-ext--strip-accents
-            argument: TEXT
-            description: '[default: ''null'']'
+              - --p-force
+              - --p-no-force
+            argument: ""
+            description: 'Force rewriting of existing files. Must be used when output files with the provided name already exist. [default: False]'
           - names:
-              - --p-feat-ext--tokenizer
-            argument: TEXT
-            description: '[default: ''null'']'
+              - --p-limit
+            argument: INTEGER
+            description: How many candidate regions (contig or transcript) to consider per BUSCO.
           - names:
-              - --p-feat-ext--decode-error
-            argument: TEXT
-            description: '[default: ''strict'']'
+              - --p-long
+              - --p-no-long
+            argument: ""
+            description: 'Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms.'
           - names:
-              - --p-feat-ext--encoding
+              - --p-metaeuk-parameters
             argument: TEXT
-            description: '[default: ''utf-8'']'
+            description: 'Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single string with no white space, with each argument separated by a comma. Example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. [optional]'
           - names:
-              - --p-feat-ext--input
+              - --p-metaeuk-rerun-parameters
             argument: TEXT
-            description: '[default: ''content'']'
+            description: 'Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma. Example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. [optional]'
           - names:
-              - --p-feat-ext--lowercase
-              - --p-no-feat-ext--lowercase
+              - --p-miniprot
+              - --p-no-miniprot
             argument: ""
-            description: '[default: True]'
-          - names:
-              - --p-feat-ext--n-features
-            argument: INTEGER
-            description: '[default: 8192]'
+            description: Use miniprot gene predictor for eukaryote runs.
           - names:
-              - --p-feat-ext--ngram-range
-            argument: TEXT
-            description: '[default: ''[7, 7]'']'
+              - --p-scaffold-composition
+              - --p-no-scaffold-composition
+            argument: ""
+            description: 'Writes ACGTN content per scaffold to a file `scaffold_composition.txt`. [default: False]'
           - names:
-              - --p-feat-ext--norm
-            argument: TEXT
-            description: '[default: ''l2'']'
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the contigs into.
           - names:
-              - --p-feat-ext--token-pattern
-            argument: TEXT
-            description: '[default: ''(?u)\\b\\w\\w+\\b'']'
+              - --o-results-table
+            argument: ARTIFACT
+            description: BUSCO result table. [required]
           - names:
-              - --o-classifier
-            argument: ARTIFACT TaxonomicClassifier
-            description: '[required]'
+              - --o-visualization
+            argument: VISUALIZATION
+            description: Visualization of the BUSCO results. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5248,6 +10110,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -5260,30 +10142,14 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: fit-classifier-sklearn
-        description: Train an almost arbitrary scikit-learn classifier
-        usage: qiime feature-classifier fit-classifier-sklearn [OPTIONS]
+      - name: fetch-diamond-db
+        description: Fetch the complete Diamond database necessary to run the eggnog-diamond-search action.
+        usage: qiime moshpit fetch-diamond-db [OPTIONS]
         options:
           - names:
-              - --i-reference-reads
-            argument: ARTIFACT FeatureData[Sequence]
-            description: '[required]'
-          - names:
-              - --i-reference-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: '[required]'
-          - names:
-              - --i-class-weight
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: '[optional]'
-          - names:
-              - --p-classifier-specification
-            argument: TEXT
-            description: '[required]'
-          - names:
-              - --o-classifier
-            argument: ARTIFACT TaxonomicClassifier
-            description: '[required]'
+              - --o-diamond-db
+            argument: ARTIFACT
+            description: Complete Diamond reference database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5305,18 +10171,14 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: makeblastdb
-        description: Make BLAST database.
-        usage: qiime feature-classifier makeblastdb [OPTIONS]
+      - name: fetch-eggnog-db
+        description: Fetch the databases necessary to run the eggnog-annotate action.
+        usage: qiime moshpit fetch-eggnog-db [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Input reference sequences. [required]
-          - names:
-              - --o-database
+              - --o-eggnog-db
             argument: ARTIFACT
-            description: Output BLAST database.
+            description: Artifact containing the eggNOG annotation database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5338,57 +10200,14 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: vsearch-global
-        description: VSEARCH global alignment search
-        usage: qiime feature-classifier vsearch-global [OPTIONS]
+      - name: fetch-eggnog-proteins
+        description: Fetch the databases necessary to run the build-eggnog-diamond-db action.
+        usage: qiime moshpit fetch-eggnog-proteins [OPTIONS]
         options:
           - names:
-              - --i-query
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Query Sequences. [required]
-          - names:
-              - --i-reference-reads
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequences. [required]
-          - names:
-              - --p-perc-identity
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: Reject match if percent identity to query is lower.
-          - names:
-              - --p-query-cov
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: 'Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8]'
-          - names:
-              - --p-strand
-            argument: TEXT Choices('both', 'plus')
-            description: Align against reference sequences in forward ("plus") or both directions ("both").
-          - names:
-              - --p-search-exact
-              - --p-no-search-exact
-            argument: ""
-            description: 'Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity, query-cov, maxaccepts, and maxrejects settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False]'
-          - names:
-              - --p-top-hits-only
-              - --p-no-top-hits-only
-            argument: ""
-            description: 'Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False]'
-          - names:
-              - --p-output-no-hits
-              - --p-no-output-no-hits
-            argument: ""
-            description: 'Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs.'
-          - names:
-              - --p-weak-id
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: 'Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0]'
-          - names:
-              - --p-threads
-            argument: NTHREADS
-            description: 'Number of threads to use for job parallelization. Pass 0 to use one per available CPU. [default: 1]'
-          - names:
-              - --o-search-results
+              - --o-eggnog-proteins
             argument: ARTIFACT
-            description: FeatureData[BLAST6] Top hits for each query. [required]
+            description: eggNOG database of protein sequences and their corresponding taxonomy information. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5410,51 +10229,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: feature-table
-    description: Plugin for working with sample by feature tables.
-    usage: qiime feature-table [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: core-features
-        description: Identify core features in table
-        usage: qiime feature-table core-features [OPTIONS]
+      - name: fetch-kaiju-db
+        description: Fetch Kaiju database.
+        usage: qiime moshpit fetch-kaiju-db [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table to use in core features calculations. [required]
-          - names:
-              - --p-min-fraction
-            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
-            description: 'The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 0.5]'
-          - names:
-              - --p-max-fraction
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: 'The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 1.0]'
-          - names:
-              - --p-steps
-            argument: INTEGER
-            description: The number of steps to take between `min-fraction` and
+              - --p-database-type
+            argument: '{nr, nr_euk, refseq, fungi, viruses, plasmids, progenomes, rvdb}'
+            description: Type of database to be downloaded. [required]
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-database
+            argument: ARTIFACT
+            description: Kaiju database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5476,57 +10262,60 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-features
-        description: Filter features from table
-        usage: qiime feature-table filter-features [OPTIONS]
+      - name: fetch-ncbi-taxonomy
+        description: Fetch NCBI reference taxonomy
+        usage: qiime moshpit fetch-ncbi-taxonomy [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table from which features should be filtered. [required]
+              - --o-taxonomy
+            argument: ARTIFACT
+            description: NCBI reference taxonomy. [required]
           - names:
-              - --p-min-frequency
-            argument: INTEGER
-            description: 'The minimum total frequency that a feature must have to be retained. [default: 0]'
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-max-frequency
-            argument: INTEGER
-            description: The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-min-samples
-            argument: INTEGER
-            description: 'The minimum number of samples that a feature must be observed in to be retained. [default: 0]'
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-max-samples
-            argument: INTEGER
-            description: The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied). [optional]
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: filter-derep-mags
+        description: Filter dereplicated MAGs.
+        usage: qiime moshpit filter-derep-mags [OPTIONS]
+        options:
+          - names:
+              - --i-mags
+            argument: ARTIFACT
+            description: Dereplicated MAGs to filter. [required]
           - names:
               - --m-metadata-file
             argument: METADATA...
-            description: Feature metadata used with `where` parameter when selecting features to retain, or with `exclude-ids` when selecting features to discard.
+            description: Sample metadata indicating which MAG ids to filter. [required]
           - names:
               - --p-where
             argument: TEXT
-            description: SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the feature table will be retained. [optional]
+            description: Optional SQLite WHERE clause specifying MAG metadata criteria that must be met to be included in the filtered data. If not provided, all MAGs in `metadata` that are also in the MAG data will be retained.
           - names:
               - --p-exclude-ids
               - --p-no-exclude-ids
             argument: ""
-            description: 'If true, the features selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. [default: False]'
-          - names:
-              - --p-filter-empty-samples
-              - --p-no-filter-empty-samples
-            argument: ""
-            description: 'If true, drop any samples where none of the retained features are present. [default: True]'
-          - names:
-              - --p-allow-empty-table
-              - --p-no-allow-empty-table
-            argument: ""
-            description: 'If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]'
+            description: 'Defaults to False. If True, the MAGs selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]'
           - names:
-              - --o-filtered-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting feature table filtered by feature. [required]
+              - --o-filtered-mags
+            argument: ARTIFACT
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -5548,31 +10337,39 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-features-conditionally
-        description: Filter features from a table based on abundance and prevalence
-        usage: qiime feature-table filter-features-conditionally [OPTIONS]
+      - name: filter-mags
+        description: Filter MAGs.
+        usage: qiime moshpit filter-mags [OPTIONS]
         options:
           - names:
-              - --i-table
+              - --i-mags
             argument: ARTIFACT
-            description: The feature table from which features should be filtered. [required]
+            description: MAGs to filter. [required]
           - names:
-              - --p-abundance
-            argument: PROPORTION
-            description: The minimum relative abundance for a feature to be retained. [required]
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata indicating which MAG ids to filter. [required]
           - names:
-              - --p-prevalence
-            argument: PROPORTION
-            description: The minimum portion of samples that a feature must have a relative abundance of at least `abundance` to be retained. [required]
+              - --p-where
+            argument: TEXT
+            description: Optional SQLite WHERE clause specifying MAG metadata criteria that must be met to be included in the filtered data. If not provided, all MAGs in `metadata` that are also in the MAG data will be retained.
           - names:
-              - --p-allow-empty-table
-              - --p-no-allow-empty-table
+              - --p-exclude-ids
+              - --p-no-exclude-ids
             argument: ""
-            description: 'If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]'
+            description: 'Defaults to False. If True, the MAGs selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]'
           - names:
-              - --o-filtered-table
+              - --p-on
+            argument: TEXT Choices('sample', 'mag')
+            description: Whether to filter based on sample or MAG metadata.
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: (multiple Sample metadata indicating which MAG ids to filter.
+          - names:
+              - --o-filtered-mags
             argument: ARTIFACT
-            description: The resulting feature table filtered by feature. [required]
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -5594,57 +10391,55 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-samples
-        description: Filter samples from table
-        usage: qiime feature-table filter-samples [OPTIONS]
+      - name: get-feature-lengths
+        description: Get feature lengths.
+        usage: qiime moshpit get-feature-lengths [OPTIONS]
         options:
           - names:
-            - --i-table
+              - --i-features
             argument: ARTIFACT
-            description: The feature table from which samples should be filtered. [required]
-          - names:
-              - --p-min-frequency
-            argument: INTEGER
-            description: 'The minimum total frequency that a sample must have to be retained. [default: 0]'
-          - names:
-              - --p-max-frequency
-            argument: INTEGER
-            description: The maximum total frequency that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]
+            description: Features to get lengths for. [required]
           - names:
-              - --p-min-features
-            argument: INTEGER
-            description: 'The minimum number of features that a sample must have to be retained. [default: 0]'
+              - --o-lengths
+            argument: ARTIFACT
+            description:  Feature lengths. [required]
           - names:
-              - --p-max-features
-            argument: INTEGER
-            description: The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied). [optional]
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude-ids` when selecting samples to discard.
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-where
-            argument: TEXT
-            description: SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. [optional]
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-exclude-ids
-              - --p-no-exclude-ids
+              - --citations
             argument: ""
-            description: 'If true, the samples selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. [default: False]'
+            description: Show citations and exit.
           - names:
-              - --p-filter-empty-features
-              - --p-no-filter-empty-features
+              - --help
             argument: ""
-            description: 'If true, features which are not present in any retained samples are dropped. [default: True]'
+            description: Show this message and exit.
+      - name: inspect-kraken2-db
+        description: Inspect a Kraken 2 database.
+        usage: qiime moshpit inspect-kraken2-db [OPTIONS]
+        options:
           - names:
-              - --p-allow-empty-table
-              - --p-no-allow-empty-table
-            argument: ""
-            description: 'If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty. [default: False]'
+              - --i-db
+            argument: ARTIFACT
+            description: The Kraken 2 database for which to generate the report. [required]
           - names:
-              - --o-filtered-table
+              - --p-threads
+            argument: INTEGER
+            description: 'The number of threads to use.   Range(1, None) [default: 1]'
+          - names:
+              - --o-report
             argument: ARTIFACT
-            description: The resulting feature table filtered by sample. [required]
+            description: The report of the supplied database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5666,35 +10461,26 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-seqs
-        description: Filter features from sequences
-        usage: qiime feature-table filter-seqs [OPTIONS]
+      - name: kraken2-to-features
+        description: Select downstream features from Kraken 2
+        usage: qiime moshpit kraken2-to-features [OPTIONS]
         options:
           - names:
-              - --i-data
-            argument: ARTIFACT FeatureData[Sequence¹ | AlignedSequence²]
-            description: The sequences from which features should be filtered. [required]
-          - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Table containing feature ids used for id-based filtering. [optional]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Feature metadata used for id-based filtering, with `where` parameter when selecting features to retain, or with `exclude-ids` when selecting features to discard.
+              - --i-reports
+            argument: ARTIFACT
+            description: Per-sample Kraken 2 reports. [required]
           - names:
-              - --p-where
-            argument: TEXT
-            description: SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences will be retained. [optional]
+              - --p-coverage-threshold
+            argument: NUMBER
+            description: 'The minimum percent coverage required to produce a feature. [default: 0.1]'
           - names:
-              - --p-exclude-ids
-              - --p-no-exclude-ids
-            argument: ""
-            description: 'If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained. [default: False]'
+              - --o-table
+            argument: ARTIFACT
+            description: A presence/absence table of selected features. The features are not of even ranks, but will be the most specific rank available. [required]
           - names:
-              - --o-filtered-data
-            argument: ARTIFACT FeatureData[Sequence¹ | AlignedSequence²]
-            description: The resulting filtered sequences. [required]
+              - --o-taxonomy
+            argument: ARTIFACT
+            description: Infra-clade ranks are ignored unless they are strain-level. Missing internal ranks are annotated by their next most specific rank, with the exception of k__Bacteria and k__Archaea which match their domain's name. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5716,31 +10502,26 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: group
-        description: Group samples or features by a metadata column
-        usage: qiime feature-table group [OPTIONS]
+      - name: kraken2-to-mag-features
+        description: Select downstream MAG features from Kraken 2
+        usage: qiime moshpit kraken2-to-mag-features [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The table to group samples or features on. [required]
-          - names:
-              - --p-axis
-            argument: TEXT Choices('feature', 'sample')
-            description: Along which axis to group. Each ID in the given axis must exist in `metadata`. [required]
+              - --i-reports
+            argument: ARTIFACT
+            description: Per-sample Kraken 2 reports. [required]
           - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: A column defining the groups. Each unique value will become a new ID for the table on the given `axis`.
+              - --i-hits
+            argument: ARTIFACT
+            description: Per-sample Kraken 2 output files. [required]
           - names:
-              - --p-mode
-            argument: TEXT Choices('mean-ceiling', 'median-ceiling', 'sum')
-            description: How to combine samples or features within a group. `sum` will sum the frequencies across all samples or features within a group; `mean-ceiling` will take the ceiling of the mean of these frequencies; `median-ceiling` will take the ceiling of the median of these frequencies. [required]
+              - --p-coverage-threshold
+            argument: NUMBER
+            description: 'The minimum percent coverage required to produce a feature. [default: 0.1]'
           - names:
-              - --o-grouped-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: A table that has been grouped along the given `axis`. IDs on that axis are replaced by values in the `metadata` column. [required]
+              - --o-taxonomy
+            argument: ARTIFACT
+            description: Infra-clade ranks are ignored unless they are strain-level. Missing internal ranks are annotated by their next most specific rank, with the exception of k__Bacteria and k__Archaea which match their domain's name. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5762,46 +10543,21 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: heatmap
-        description: Generate a heatmap representation of a feature table
-        usage: qiime feature-table heatmap [OPTIONS]
+      - name: partition-feature-data-mags
+        description: Partition MAGs
+        usage: qiime moshpit partition-feature-data-mags [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table to visualize. [required]
-          - names:
-              - --m-sample-metadata-file
-            argument: ""
-            description: METADATA
-          - names:
-              - --m-sample-metadata-column
-            argument: COLUMN  MetadataColumn[Categorical]
-            description: Annotate the sample IDs with these sample metadata values. When metadata is present and `cluster`='feature', samples will be sorted by the metadata values. [optional]
-          - names:
-              - --m-feature-metadata-file
-            argument: ""
-            description: METADATA
-          - names:
-              - --m-feature-metadata-column
-            argument: COLUMN  MetadataColumn[Categorical]
-            description: Annotate the feature IDs with these feature metadata values. When metadata is present and `cluster`='sample', features will be sorted by the metadata values. [optional]
-          - names:
-              - --p-normalize
-              - --p-no-normalize
-            argument: ""
-            description: Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table.
-          - names:
-              - --p-title
-            argument: TEXT
-            description: Optional custom plot title. [optional]
+              - --i-mags
+            argument: ARTIFACT
+            description: MAGs to partition. [required]
           - names:
-              - --p-cluster
-            argument: TEXT Choices('both', 'features', 'none', 'samples')
-            description: 'Specify which axes to cluster. [default: ''both'']'
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the MAGs into.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
+              - --o-partitioned-mags
+            argument: ARTIFACTS...
             description: '[required]'
           - names:
               - --output-dir
@@ -5824,10 +10580,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: merge
-        description: Combine multiple tables
-        usage: qiime feature-table merge [OPTIONS]
+      - name: partition-orthologs
+        description: Partition orthologs
+        usage: qiime moshpit partition-orthologs [OPTIONS]
         options:
+          - names:
+              - --i-orthologs
+            argument: ARTIFACT
+            description: The orthologs to partition. [required]
+          - names:
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the MAGs into.
+          - names:
+              - --o-partitioned-orthologs
+            argument: ARTIFACTS...
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -5849,18 +10617,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: merge-seqs
-        description: Combine collections of feature sequences
-        usage: qiime feature-table merge-seqs [OPTIONS]
+      - name: partition-sample-data-mags
+        description: Partition MAGs
+        usage: qiime moshpit partition-sample-data-mags [OPTIONS]
         options:
           - names:
-              - --i-data
-            argument: ARTIFACTS... List[FeatureData[Sequence]]
-            description: The collection of feature sequences to be merged.
+              - --i-mags
+            argument: ARTIFACT
+            description: The MAGs to partition. [required]
+          - names:
+              - --p-num-partitions
+            argument: INTEGER
+            description: Range(1, None) The number of partitions to split the MAGs into.
           - names:
-              - --o-merged-data
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The resulting collection of feature sequences containing all feature sequences provided. [required]
+              - --o-partitioned-mags
+            argument: ARTIFACTS...
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -5882,18 +10654,30 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: merge-taxa
-        description: Combine collections of feature taxonomies
-        usage: qiime feature-table merge-taxa [OPTIONS]
+      - name: predict-genes-prodigal
+        description: Predict gene sequences from MAGs using Prodigal.
+        usage: qiime moshpit predict-genes-prodigal [OPTIONS]
         options:
           - names:
-              - --i-data
-            argument: ARTIFACTS... List[FeatureData[Taxonomy]]
-            description: The collection of feature taxonomies to be merged.
+              - --i-mags
+            argument: ARTIFACT
+            description: MAGs for which one wishes to predict genes. [required]
           - names:
-              - --o-merged-data
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: The resulting collection of feature taxonomies containing all feature taxonomies provided.
+              - --p-translation-table-number
+            argument: TEXT
+            description: Translation table to be used to translate genes into a sequence of amino acids..
+          - names:
+              - --o-loci
+            argument: ARTIFACT
+            description: Gene coordinates files (one per MAG) listing the location of each predicted gene as well as some additional scoring information. [required]
+          - names:
+              - --o-genes
+            argument: ARTIFACT
+            description: Fasta files (one per MAG) with the nucleotide sequences of the predicted genes. [required]
+          - names:
+              - --o-proteins
+            argument: ARTIFACT GenomeData[Proteins]
+            description: Fasta files (one per MAG) with the protein translation of the predicted genes. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5915,18 +10699,68 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: presence-absence
-        description: Convert to presence/absence
-        usage: qiime feature-table presence-absence [OPTIONS]
+  - name: phylogeny
+    description: Plugin for generating and manipulating phylogenies.
+    usage: qiime phylogeny [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: align-to-tree-mafft-fasttree
+        description: Build a phylogenetic tree using fasttree and
+        usage: qiime phylogeny align-to-tree-mafft-fasttree [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency | RelativeFrequency]
-            description: The feature table to be converted into presence/absence abundances. [required]
+              - --i-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The sequences to be used for creating a fasttree based rooted phylogenetic tree. [required]
           - names:
-              - --o-presence-absence-table
-            argument: ARTIFACT FeatureTable[PresenceAbsence]
-            description: The resulting presence/absence feature table.
+              - --p-n-threads
+            argument: NTHREADS
+            description: 'The number of threads. (Use `auto` to automatically use all available cores) This value is used when aligning the sequences and creating the tree with fasttree. [default: 1]'
+          - names:
+              - --p-mask-max-gap-frequency
+            argument: PROPORTION Range(0, 1, inclusive_end=True)
+            description: The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences.
+          - names:
+              - --p-mask-min-conservation
+            argument: PROPORTION Range(0, 1, inclusive_end=True)
+            description: The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences.
+          - names:
+              - --p-parttree
+              - --p-no-parttree
+            argument: ""
+            description: 'This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. [default: False]'
+          - names:
+              - --o-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: The aligned sequences. [required]
+          - names:
+              - --o-masked-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: The masked alignment. [required]
+          - names:
+              - --o-tree
+            argument: ARTIFACT
+            description: The unrooted phylogenetic tree.
+          - names:
+              - --o-rooted-tree
+            argument: ARTIFACT
+            description: Phylogeny[Rooted] The rooted phylogenetic tree. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5936,6 +10770,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -5948,27 +10802,67 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: rarefy
-        description: Rarefy table
-        usage: qiime feature-table rarefy [OPTIONS]
+      - name: align-to-tree-mafft-iqtree
+        description: Build a phylogenetic tree using iqtree and
+        usage: qiime phylogeny align-to-tree-mafft-iqtree [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table to be rarefied. [required]
+              - --i-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]
           - names:
-              - --p-sampling-depth
-            argument: INTEGER
-            description: The total frequency that each sample should be rarefied to. [required]
+              - --p-n-threads
+            argument: NTHREADS
+            description: The number of threads. (Use 0 to automatically use all available cores This value is used when aligning the sequences and creating the tree with iqtree.
           - names:
-              - --p-with-replacement
-              - --p-no-with-replacement
+              - --p-mask-max-gap-frequency
+            argument: PROPORTION Range(0, 1, inclusive_end=True)
+            description: The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences.
+          - names:
+              - --p-mask-min-conservation
+            argument: PROPORTION Range(0, 1, inclusive_end=True)
+            description: The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences.
+          - names:
+              - --p-substitution-model
+            argument: TEXT
+            description: Model of Nucleotide Substitution. If not provided, IQ-TREE will determine the best fit substitution model automatically.
+          - names:
+              - --p-fast
+              - --p-no-fast
             argument: ""
-            description: 'Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]'
+            description: 'Fast search to resemble FastTree. [default: False]'
           - names:
-              - --o-rarefied-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting rarefied feature table. [required]
+              - --p-alrt
+            argument: INTEGER
+            description: Single branch test method. Number of bootstrap replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is required.
+          - names:
+              - --p-stop-iter
+            argument: INTEGER
+            description: Number of unsuccessful iterations to stop. If not set, program defaults will be used.
+          - names:
+              - --p-perturb-nni-strength
+            argument: NUMBER
+            description: Perturbation strength for randomized NNI.
+          - names:
+              - --p-seed
+            argument: INTEGER
+            description: Random number seed for the iqtree parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]
+          - names:
+              - --o-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: The aligned sequences. [required]
+          - names:
+              - --o-masked-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: The masked alignment. [required]
+          - names:
+              - --o-tree
+            argument: ARTIFACT
+            description: The unrooted phylogenetic tree.
+          - names:
+              - --o-rooted-tree
+            argument: ARTIFACT
+            description: Phylogeny[Rooted] The rooted phylogenetic tree. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -5978,6 +10872,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -5990,18 +10904,55 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: relative-frequency
-        description: Convert to relative frequencies
-        usage: qiime feature-table relative-frequency [OPTIONS]
+      - name: align-to-tree-mafft-raxml
+        description: Build a phylogenetic tree using raxml and
+        usage: qiime phylogeny align-to-tree-mafft-raxml [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table to be converted into relative frequencies. [required]
+              - --i-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]
+          - names:
+              - --p-n-threads
+            argument: NTHREADS
+            description: 'The number of threads. (Use `all` to automatically use all available cores. This value is used when aligning the sequences and creating the tree with iqtree. [default: 1]'
+          - names:
+              - --p-mask-max-gap-frequency
+            argument: PROPORTION Range(0, 1, inclusive_end=True)
+            description: The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences.
+          - names:
+              - --p-mask-min-conservation
+            argument: PROPORTION Range(0, 1, inclusive_end=True)
+            description: The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences.
+          - names:
+              - --p-parttree
+              - --p-no-parttree
+            argument: ""
+            description: 'This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. NOTE: if using this option, it is recomended that only the CAT-based substitution models of RAxML be considered for this pipeline.'
+          - names:
+              - --p-seed
+            argument: INTEGER
+            description: Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen.
+          - names:
+              - --p-raxml-version
+            argument: TEXT Choices('Standard', 'SSE3', 'AVX2')
+            description: Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version.
+          - names:
+              - --o-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: The aligned sequences. [required]
+          - names:
+              - --o-masked-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: The masked alignment. [required]
+          - names:
+              - --o-tree
+            argument: ARTIFACT
+            description: The unrooted phylogenetic tree.
           - names:
-              - --o-relative-frequency-table
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: The resulting relative frequency feature table.
+              - --o-rooted-tree
+            argument: ARTIFACT
+            description: Phylogeny[Rooted] The rooted phylogenetic tree. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -6012,44 +10963,25 @@ subcommands:
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
-          - names:
-              - --citations
-            argument: ""
-            description: Show citations and exit.
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
           - names:
-              - --help
+              - --no-recycle
             argument: ""
-            description: Show this message and exit.
-      - name: rename-ids
-        description: Renames sample or feature ids in a table
-        usage: qiime feature-table rename-ids [OPTIONS]
-        options:
-          - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: A metadata column defining the new ids. Each original id must map to a new unique id. If strict mode is used, then every id in the original table must have a new id.
-          - names:
-              - --p-axis
-            argument: TEXT Choices('feature', 'sample')
-            description: 'Along which axis to rename the ids. [default: ''sample'']'
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
           - names:
-              - --p-strict
-              - --p-no-strict
+              - --parallel
             argument: ""
-            description: 'Whether the naming needs to be strict (each id in the table must have a new id). Otherwise, only the ids described in `metadata` will be renamed and the others will keep their original id names. [default: False]'
+            description: Execute your action in parallel. This flag will use your default parallel config.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -6062,20 +10994,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: split
-        description: Split one feature table into many
-        usage: qiime feature-table split [OPTIONS]
+      - name: fasttree
+        description: Construct a phylogenetic tree with FastTree.
+        usage: qiime phylogeny fasttree [OPTIONS]
         options:
           - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: A column defining the groups. Each unique value will define a split feature table. [required]
+              - --i-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: Aligned sequences to be used for phylogenetic reconstruction. [required]
           - names:
-              - --p-filter-empty-features
-              - --p-no-filter-empty-features
-            argument: ""
-            description: 'If true, features which are not present in a split feature table are dropped. [default: True]'
+              - --p-n-threads
+            argument: NTHREADS
+            description: 'The number of threads. Using more than one thread runs the non-deterministic variant of `FastTree` (`FastTreeMP`), and may result in a different tree than single-threading. See http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto` to automatically use all available cores) [default: 1]'
+          - names:
+              - --o-tree
+            argument: ARTIFACT
+            description: The resulting phylogenetic tree.
           - names:
               - --output-dir
             argument: PATH
@@ -6097,26 +11031,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: subsample-ids
-        description: Subsample table
-        usage: qiime feature-table subsample-ids [OPTIONS]
+      - name: filter-table
+        description: Remove features from table if they're not
+        usage: qiime phylogeny filter-table [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The feature table to be sampled. [required]
-          - names:
-              - --p-subsampling-depth
-            argument: ""
-            description: INTEGER
-          - names:
-              - --p-axis
-            argument: TEXT Choices('sample', 'feature')
-            description: The axis to sample over. If "sample" then samples will be randomly selected to be retained. If "feature" then a random set of features will be selected to be retained. [required]
+              - --i-tree
+            argument: ARTIFACT Phylogeny[Rooted | Unrooted]
+            description: Tree where tip identifiers are the feature identifiers that should be retained in the table. [required]
           - names:
-              - --o-sampled-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The resulting subsampled feature table. [required]
+              - --i-table
+            argument: ARTIFACT FeatureTable
+            description: Feature table that features should be filtered from.
           - names:
               - --output-dir
             argument: PATH
@@ -6138,22 +11064,30 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: summarize
-        description: Summarize table
-        usage: qiime feature-table summarize [OPTIONS]
+      - name: filter-tree
+        description: Remove features from tree based on metadata
+        usage: qiime phylogeny filter-tree [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency | PresenceAbsence]
-            description: The feature table to be summarized. [required]
+              - --i-tree
+            argument: ARTIFACT Phylogeny[Rooted¹ | Unrooted²]
+            description: Tree that should be filtered [required]
           - names:
-              - --m-sample-metadata-file
+              -  --i-table
+            argument: ARTIFACT
+            description: Feature table which contains the identifier that should be retained in the tree
+          - names:
+              - --m-metadata-file
             argument: METADATA...
-            description: The sample metadata.
+            description: Feature metadata to use with the 'where' statement or to select tips to be retained.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --p-where
+            argument: TEXT
+            description: SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. [optional]
+          - names:
+              - --o-filtered-tree
+            argument: ARTIFACT Phylogeny[Rooted¹ | Unrooted²]
+            description: The resulting phylogenetic tree. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -6175,87 +11109,94 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: summarize-plus
-        description: Summarize table plus
-        usage: qiime feature-table summarize-plus [OPTIONS]
+      - name: iqtree
+        description: Construct a phylogenetic tree with IQ-TREE.
+        usage: qiime phylogeny iqtree [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency | PresenceAbsence]
-            description: The feature table to be summarized. [required]
+              - --i-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: Aligned sequences to be used for phylogenetic reconstruction. [required]
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: The sample metadata.
+              - --p-seed
+            argument: INTEGER
+            description: Random number seed. If not set, program defaults
           - names:
-              - --o-feature-frequencies
-            argument: ARTIFACT
-            description: Per-sample and total frequencies per feature. [required]
+              - --p-n-cores
+            argument: NTHREADS
+            description: The number of cores to use for parallel processing.
           - names:
-              - --o-sample-frequencies
-            argument: ARTIFACT
-            description: Observed feature count and total frequencies per sample. [required]
+              - --p-n-cores-max
+            argument: NTHREADS
+            description: Limits the maximum number of cores to be used when
           - names:
-              - --o-summary
-            argument: VISUALIZATION
-            description: Visual summary of feature table [required]
+              - --p-n-runs
+            argument: INTEGER
+            description: Number of indepedent runs. Multiple independent
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-substitution-model
+            argument: TEXT
+            description: Model of Nucleotide Substitution.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --p-n-init-pars-trees
+            argument: INTEGER
+            description: Number of initial parsimony trees.
           - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+              - --p-n-top-init-trees
+            argument: INTEGER
+            description: Number of top initial trees.
           - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+              - --p-n-best-retain-trees
+            argument: INTEGER
+            description: Number of best trees retained during search.
           - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
+              - --p-n-iter
+            argument: INTEGER
+            description: Fix number of iterations to stop.
           - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
+              - --p-stop-iter
+            argument: INTEGER
+            description: Number of unsuccessful iterations to stop.
           - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+              - --p-perturb-nni-strength
+            argument: NUMBER
+            description: Perturbation strength for randomized NNI.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-spr-radius
+            argument: INTEGER
+            description: Radius for parsimony SPR search.
           - names:
-              - --citations
+              - --p-allnni
+              - --p-no-allnni
             argument: ""
-            description: Show citations and exit.
+            description: 'Perform more thorough NNI search. [default: False]'
           - names:
-              - --help
+              - --p-fast
+              - --p-no-fast
             argument: ""
-            description: Show this message and exit.
-      - name: tabulate-feature-frequencies
-        description: Tabulate feature frequencies
-        usage: qiime feature-table tabulate-feature-frequencies [OPTIONS]
-        options:
+            description: 'Fast search to resemble FastTree. [default: False]'
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable
-            description: The input feature table. [required]
+              - --p-alrt
+            argument: INTEGER
+            description: Single branch test method. Number of bootstrap
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTableFrequency | PresenceAbsence |   RelativeFrequency
-            description: The input feature table. [required]
+              - --p-abayes
+              - --p-no-abayes
+            argument: ""
+            description: Single branch test method. Approximate Bayes test.
           - names:
-              - --o-feature-frequencies
+              - --p-lbp
+            argument: INTEGER
+            description: Single branch test method. Number of bootstrap
+          - names:
+              - --p-safe
+              - --p-no-safe
+            argument: ""
+            description: Safe likelihood kernel to avoid numerical
+          - names:
+              - --o-tree
             argument: ARTIFACT
-            description: ImmutableMetadata Per-sample and total frequencies per feature.
+            description: The resulting phylogenetic tree.
           - names:
               - --output-dir
             argument: PATH
@@ -6277,154 +11218,110 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: tabulate-sample-frequencies
-        description: Tabulate sample frequencies
-        usage: qiime feature-table tabulate-sample-frequencies [OPTIONS]
+      - name: iqtree-ultrafast-bootstrap
+        description: Construct a phylogenetic tree with IQ-TREE
+        usage: qiime phylogeny iqtree-ultrafast-bootstrap [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable
-            description: The input feature table. [required]
+              - --i-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: Aligned sequences to be used for phylogenetic reconstruction. [required]
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTableFrequency | PresenceAbsence |   RelativeFrequency
-            description: The input feature table. [required]
+              - --p-seed
+            argument: INTEGER
+            description: Random number seed. If not set, program defaults
           - names:
-              - --o-sample-frequencies
-            argument: ARTIFACT
-            description: ImmutableMetadata Observed feature count and total frequencies per
+              - --p-n-cores
+            argument: NTHREADS
+            description: The number of cores to use for parallel processing.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-n-cores-max
+            argument: NTHREADS
+            description: Limits the maximum number of cores to be used when
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --p-n-runs
+            argument: INTEGER
+            description: Number of indepedent runs. Multiple independent
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-substitution-model
+            argument: TEXT
+            description: Model of Nucleotide Substitution.
           - names:
-              - --citations
-            argument: ""
-            description: Show citations and exit.
+              - --p-bootstrap-replicates
+            argument: INTEGER
+            description: The number of bootstrap searches to perform.
           - names:
-              - --help
-            argument: ""
-            description: Show this message and exit.
-      - name: tabulate-seqs
-        description: View sequence associated with each feature
-        usage: qiime feature-table tabulate-seqs [OPTIONS]
-        options:
+              - --p-n-init-pars-trees
+            argument: INTEGER
+            description: Number of initial parsimony trees.
           - names:
-              - --i-data
-            argument: ARTIFACT FeatureData[Sequence | AlignedSequence]
-            description: The feature sequences to be tabulated. [required]
+              - --p-n-top-init-trees
+            argument: INTEGER
+            description: Number of top initial trees.
           - names:
-              - --i-taxonomy
-            argument: ARTIFACTS... Collection[FeatureData[Taxonomy]]
-            description: The taxonomic classifications of the tabulated features. [optional]
+              - --p-n-best-retain-trees
+            argument: INTEGER
+            description: Number of best trees retained during search.
           - names:
-              - --p-merge-method
-            argument: TEXT Choices('strict', 'union', 'intersect')
-            description: 'Method that joins data sets [default: ''strict'']'
+              - --p-stop-iter
+            argument: INTEGER
+            description: Number of unsuccessful iterations to stop.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: "[required]"
+              - --p-perturb-nni-strength
+            argument: NUMBER
+            description: Perturbation strength for randomized NNI.
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Any additional metadata for the tabulated features.
+              - --p-spr-radius
+            argument: INTEGER
+            description: Radius for parsimony SPR search.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-n-max-ufboot-iter
+            argument: INTEGER
+            description: Maximum number of iterations.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --p-n-ufboot-steps
+            argument: INTEGER
+            description: Number of iterations for UFBoot stopping rule.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-min-cor-ufboot
+            argument: NUMBER
+            description: Minimum correlation coefficient.
           - names:
-              - --citations
-            argument: ""
-            description: Show citations and exit.
+              - --p-ep-break-ufboot
+            argument: NUMBER
+            description: Epsilon value to break tie.
           - names:
-              - --help
+              - --p-allnni
+              - --p-no-allnni
             argument: ""
-            description: Show this message and exit.
-      - name: transpose
-        description: Transpose a feature table.
-        usage: qiime feature-table transpose [OPTIONS]
-        options:
+            description: 'Perform more thorough NNI search. [default: False]'
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-alrt
+            argument: INTEGER
+            description: Single branch test method.
           - names:
-              - --verbose
-              - --quiet
+              - --p-abayes
+              - --p-no-abayes
             argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+            description: Single branch test method.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-lbp
+            argument: INTEGER
+            description: Single branch test method.
           - names:
-              - --citations
+              - --p-bnni
+              - --p-no-bnni
             argument: ""
-            description: Show citations and exit.
+            description: Optimize UFBoot trees by NNI on bootstrap alignment.
           - names:
-              - --help
+              - --p-safe
+              - --p-no-safe
             argument: ""
-            description: Show this message and exit.
-  - name: fragment-insertion
-    description: Plugin for extending phylogenies.
-    usage: qiime fragment-insertion [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: classify-otus-experimental
-        description: 'Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.'
-        usage: "qiime fragment-insertion classify-otus-experimental [OPTIONS]"
-        options:
-          - names:
-              - --i-representative-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The sequences used for a 'sepp' run to produce the 'tree'. [required]
+            description: Safe likelihood kernel to avoid numerical underflow.
           - names:
-              - --i-tree
+              - --o-tree
             argument: ARTIFACT
-            description: The tree resulting from inserting fragments into a
-          - names:
-              - --i-reference-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string. [required]
-          - names:
-              - --o-classification
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomic lineages for inserted fragments. [required]
+            description: The resulting phylogenetic tree.
           - names:
               - --output-dir
             argument: PATH
@@ -6446,26 +11343,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-features
-        description: Filter fragments in tree from table.
-        usage: qiime fragment-insertion filter-features [OPTIONS]
+      - name: midpoint-root
+        description: Midpoint root an unrooted phylogenetic tree.
+        usage: qiime phylogeny midpoint-root [OPTIONS]
         options:
-          - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: A feature-table which needs to filtered down to those fragments that are contained in the tree, e.g. result of a Deblur or DADA2 run. [required]
           - names:
               - --i-tree
-            argument: ARTIFACT
-            description: The tree resulting from inserting fragments into a
-          - names:
-              - --o-filtered-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: The input table minus those fragments that were not part of the tree. This feature-table can be used for downstream analyses like phylogenetic alpha- or betadiversity computation. [required]
+            argument: ARTIFACT Phylogeny[Unrooted]
+            description: The phylogenetic tree to be rooted. [required]
           - names:
-              - --o-removed-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Those fragments that got removed from the input table, because they were not part of the tree. This table is mainly used for quality control, e.g. to inspect the ratio of removed reads per sample from the input table. You can ignore this table for downstream analyses.
+              - --o-rooted-tree
+            argument: ARTIFACT
+            description: Phylogeny[Rooted] The rooted phylogenetic tree. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -6487,43 +11376,34 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: sepp
-        description: Insert fragment sequences using SEPP into reference phylogenies.
-        usage: qiime fragment-insertion sepp [OPTIONS]
+      - name: raxml
+        description: Construct a phylogenetic tree with RAxML.
+        usage: qiime phylogeny raxml [OPTIONS]
         options:
           - names:
-              - --i-representative-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The sequences to insert into the reference tree.
-          - names:
-              - --i-reference-database
-            argument: ARTIFACT SeppReferenceDatabase
-            description: The reference database to insert the representative sequences into. [required]
+              - --i-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: Aligned sequences to be used for phylogenetic reconstruction. [required]
           - names:
-              - --p-alignment-subset-size
+              - --p-seed
             argument: INTEGER
-            description: 'Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. [default: 1000]'
+            description: Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen.
           - names:
-              - --p-placement-subset-size
+              - --p-n-searches
             argument: INTEGER
-            description: 'The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. Further reading: https://github.com/smirarab/sepp/blob/master/tutorial/ sepp-tutorial.md#sample-datasets-default-parameters.'
+            description: The number of independent maximum likelihood
           - names:
-              - --p-threads
+              - --p-n-threads
             argument: NTHREADS
-            description: 'The number of threads to use. Pass 0 to use one per available core. [default: 1]'
-          - names:
-              - --p-debug
-              - --p-no-debug
-            argument: ""
-            description: 'Collect additional run information to STDOUT for debugging. Temporary directories will not be removed if run fails. [default: False]'
+            description: 'The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML. [default: 1]'
           - names:
-              - --o-tree
-            argument: ARTIFACT
-            description: The tree with inserted feature data.
+              - --p-raxml-version
+            argument: TEXT Choices('Standard', 'SSE3', 'AVX2')
+            description: Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version.
           - names:
-              - --o-placements
+              - --o-tree
             argument: ARTIFACT
-            description: Placements Information about the feature placements within the
+            description: The resulting phylogenetic tree.
           - names:
               - --output-dir
             argument: PATH
@@ -6545,61 +11425,38 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: longitudinal
-    description: Plugin for paired sample and time series analyses.
-    usage: qiime longitudinal [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: anova
-        description: ANOVA test
-        usage: qiime longitudinal anova [OPTIONS]
+      - name: raxml-rapid-bootstrap
+        description: Construct a phylogenetic tree with bootstrap
+        usage: qiime phylogeny raxml-rapid-bootstrap [OPTIONS]
         options:
           - names:
-            - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata containing formula terms. [required]
+              - --i-alignment
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: Aligned sequences to be used for phylogenetic reconstruction. [required]
           - names:
-              - --p-formula
-            argument: TEXT
-            description: R-style formula specifying the model. All terms must be present in the sample metadata or metadata-transformable artifacts and can be continuous or categorical metadata columns. Formulae will be in the format "a ~ b + c", where "a" is the metric (dependent variable) and "b" and "c" are independent covariates. Use "+" to add a variable; "+ a:b" to add an interaction between variables a and b; "*" to include a variable and all interactions; and "-" to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [required]
+              - --p-seed
+            argument: INTEGER
+            description: Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen.
           - names:
-              - --p-sstype
-            argument: TEXT Choices('I', 'II', 'III')
-            description: 'Type of sum of squares calculation to perform (I, II, or III). [default: ''II'']'
+              - --p-rapid-bootstrap-seed
+            argument: INTEGER
+            description: Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen.
           - names:
-              - --p-repeated-measures
-              - --p-no-repeated-measures
+              - --p-bootstrap-replicates
             argument: ""
-            description: 'Perform ANOVA as a repeated measures ANOVA. Implemented via statsmodels, which has the following limitations: Currently, only fully balanced within-subject designs are supported. Calculation of between-subject effects and corrections for violation of sphericity are not yet implemented. [default: False]'
+            description: INTEGER
           - names:
-              - --p-individual-id-column
-            argument: TEXT
-            description: The column containing individual ID with repeated measures to account for.This should not be included in the formula. [optional]
+              - --p-n-threads
+            argument: NTHREADS
+            description: 'The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML. [default: 1]'
           - names:
-              - --p-rm-aggregate
-              - --p-no-rm-aggregate
-            argument: ""
-            description: 'If the data set contains more than a single observation per individual id and cell of the specified model, this function will be used to aggregate the data by the mean before running the ANOVA. Only applicable for repeated measures ANOVA. [default: False]'
+              - --p-raxml-version
+            argument: TEXT Choices('Standard', 'SSE3', 'AVX2')
+            description: Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-tree
+            argument: ARTIFACT
+            description: The resulting phylogenetic tree.
           - names:
               - --output-dir
             argument: PATH
@@ -6621,83 +11478,26 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: feature-volatility
-        description: Feature volatility analysis
-        usage:  qiime longitudinal feature-volatility [OPTIONS]
+      - name: robinson-foulds
+        description: Calculate Robinson-Foulds distance between
+        usage: qiime phylogeny robinson-foulds [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Feature table containing all features that should be used for target prediction. [required]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata file containing individual-id-column. [required]
-          - names:
-              - --p-state-column
-            argument: TEXT
-            description: Metadata containing collection time (state) values for each sample. Must contain exclusively numeric values. [required]
-          - names:
-              - --p-individual-id-column
-            argument: TEXT
-            description: Metadata column containing IDs for individual subjects. [optional]
-          - names:
-              - --p-cv
-            argument: INTEGER
-            description: Number of k-fold cross-validations to perform.
-          - names:
-              - --p-random-state
-            argument: INTEGER
-            description: Seed used by random number generator. [optional]
-          - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'Number of jobs to run in parallel. [default: 1]'
-          - names:
-              - --p-n-estimators
-            argument: INTEGER
-            description: Number of trees to grow for estimation. More trees will improve predictive accuracy up to a threshold level, but will also increase time and memory requirements.
-          - names:
-              - --p-estimator
-            argument: '{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor, ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}'
-            description: Estimator method to use for sample prediction.
-          - names:
-              - --p-parameter-tuning
-              - --p-no-parameter-tuning
-            argument: ""
-            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
-          - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
-          - names:
-              - --p-importance-threshold
-            argument: VALUE
-            description: Filter feature table to exclude any features with an importance score less than this threshold.
-          - names:
-              - --p-feature-count
-            argument: VALUE
-            description: Filter feature table to include top N most important features.
-          - names:
-              - --o-filtered-table
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Feature table containing only important features. [required]
-          - names:
-              - --o-feature-importance
-            argument: ARTIFACT FeatureData[Importance]
-            description: Importance of each input feature to model accuracy. [required]
+              - --i-trees
+            argument: ARTIFACTS... List[Phylogeny[Rooted | Unrooted]]
+            description: Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric. [required]
           - names:
-              - --o-volatility-plot
-            argument: VISUALIZATION
-            description: Interactive volatility plot visualization. [required]
+              - --p-labels
+            argument: TEXT...
+            description: Labels to use for the tree names in the distance
           - names:
-              - --o-accuracy-results
-            argument: VISUALIZATION
-            description: Accuracy results visualization. [required]
+              - --p-missing-tips
+            argument: TEXT Choices('error', 'intersect-all')
+            description: 'How to handle tips that are not shared between trees. "error" will raise an error if the set of tips is not identical between all input trees. "intersect-all" will remove tips that are not shared between all trees before computing distances beteen trees. [default: ''error'']'
           - names:
-              - --o-sample-estimator
-            argument: ARTIFACT SampleEstimator[Regressor]
-            description: Trained sample regressor. [required]
+              - --o-distance-matrix
+            argument: ARTIFACT
+            description: DistanceMatrix The distances between trees as a symmetric matrix.
           - names:
               - --output-dir
             argument: PATH
@@ -6707,26 +11507,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -6739,42 +11519,43 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: first-differences
-        description: Compute first differences or difference from
-        usage: qiime longitudinal first-differences [OPTIONS]
+  - name: quality-control
+    description: Plugin for quality control of feature and sequence data.
+    usage: qiime quality-control [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: bowtie2-build
+        description: Build bowtie2 index from reference sequences.
+        usage: qiime quality-control bowtie2-build [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Feature table to optionally use for computing first differences. [optional]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata file containing individual-id-column. [required]
-          - names:
-              - --p-state-column
-            argument: TEXT
-            description: Metadata column containing state (time) variable information. [required]
-          - names:
-              - --p-individual-id-column
-            argument: TEXT
-            description: Metadata column containing IDs for individual subjects. [required]
-          - names:
-              - --p-metric
-            argument: TEXT
-            description: Numerical metadata or artifact column to test.
-          - names:
-              - --p-replicate-handling
-            argument: TEXT Choices('error', 'random', 'drop')
-            description: 'Choose how replicate samples are handled. If replicates are detected, "error" causes method to fail; "drop" will discard all replicated samples; "random" chooses one representative at random from among replicates. [default: ''error'']'
+              - --i-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Reference sequences used to build bowtie2 index.
           - names:
-              - --p-baseline
-            argument: NUMBER
-            description: A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static differences instead of first differences (which are calculated if no value is given for baseline). If a "baseline" value is provided, sample differences at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]
+              - --p-n-threads
+            argument: NTHREADS
+            description: 'Number of threads to launch.   [default: 1]'
           - names:
-              - --o-first-differences
-            argument: ARTIFACT SampleData[FirstDifferences]
-            description: Series of first differences. [required]
+              - --o-database
+            argument: ARTIFACT
+            description: Bowtie2 index.
           - names:
               - --output-dir
             argument: PATH
@@ -6796,38 +11577,38 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: first-distances
-        description: Compute first distances or distance from baseline
-        usage: qiime longitudinal first-distances [OPTIONS]
+      - name: decontam-identify
+        description: Identify contaminants
+        usage: qiime quality-control decontam-identify [OPTIONS]
         options:
           - names:
-              - --i-distance-matrix
-            argument: ARTIFACT
-            description: Matrix of distances between pairs of samples. [required]
+              - --i-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Feature table which contaminate sequences will be identified from [required]
           - names:
               - --m-metadata-file
             argument: METADATA...
-            description: Sample metadata file containing individual-id-column. [required]
+            description: metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter [required]
           - names:
-              - --p-state-column
-            argument: TEXT
-            description: Metadata column containing state (time) variable information. [required]
+              - --p-method
+            argument: TEXT Choices('combined', 'frequency', 'prevalence')
+            description: 'Select how to which method to id contaminants with; Prevalence: Utilizes control ASVs/OTUs to identify contaminants, Frequency: Utilizes sample concentration information to identify contaminants, Combined: Utilizes both Prevalence and Frequency methods when identifying contaminants [default: ''prevalence'']'
           - names:
-              - --p-individual-id-column
+              - --p-freq-concentration-column
             argument: TEXT
-            description: Metadata column containing IDs for individual subjects. [required]
+            description: Input column name that has concentration information for the samples [optional]
           - names:
-              - --p-baseline
-            argument: NUMBER
-            description: A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a "baseline" value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column.
+              - --p-prev-control-column
+            argument: TEXT
+            description: Input column name containing experimental or control sample metadata [optional]
           - names:
-              - --p-replicate-handling
-            argument: TEXT Choices('error', 'random', 'drop')
-            description: 'Choose how replicate samples are handled. If replicates are detected, "error" causes method to fail; "drop" will discard all replicated samples; "random" chooses one representative at random from among replicates. [default: ''error'']'
+              - --p-prev-control-indicator
+            argument: TEXT
+            description: indicate the control sample identifier (e.g. "control" or "blank") [optional]
           - names:
-              - --o-first-distances
-            argument: ARTIFACT SampleData[FirstDifferences]
-            description: Series of first distances. [required]
+              - --o-decontam-scores
+            argument: ARTIFACT FeatureData[DecontamScore]
+            description: The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence [required]
           - names:
               - --output-dir
             argument: PATH
@@ -6849,59 +11630,72 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: linear-mixed-effects
-        description: Linear mixed effects modeling
-        usage: qiime longitudinal linear-mixed-effects [OPTIONS]
+      - name: decontam-identify-batches
+        description: Identify contaminants in Batch Mode
+        usage: qiime quality-control decontam-identify-batches [OPTIONS]
         options:
           - names:
               - --i-table
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Feature table containing metric. [optional]
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Feature table which contaminate sequences will be identified from [required]
+          - names:
+              - --i-rep-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Representative Sequences table which contaminate seqeunces will be removed from [optional]
           - names:
               - --m-metadata-file
             argument: METADATA...
-            description: Sample metadata file containing individual-id-column. [required]
+            description: metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter [required]
           - names:
-              - --p-state-column
+              - --p-split-column
             argument: TEXT
-            description: Metadata column containing state (time) variable information. [required]
+            description: 'input metadata columns that you wish to subset the ASV table byNote: Column names must be in quotes and delimited by a space [required]'
           - names:
-              - --p-individual-id-column
-            argument: TEXT
-            description: Metadata column containing IDs for individual subjects. [required]
+              - --p-method
+            argument: TEXT Choices('combined', 'frequency', 'prevalence')
+            description: 'Select how to which method to id contaminants with; Prevalence: Utilizes control ASVs/OTUs to identify contaminants, Frequency: Utilizes sample concentration information to identify contaminants, Combined: Utilizes both Prevalence and Frequency methods when identifying contaminants [required]'
           - names:
-              - --p-metric
-            argument: TEXT
-            description: Dependent variable column name. Must be a column name located in the metadata or feature table files.
+              - --p-filter-empty-features
+              - --p-no-filter-empty-features
+            argument: ""
+            description: If true, features which are not present in a split feature table are dropped. [optional]
           - names:
-              - --p-group-columns
+              - --p-freq-concentration-column
             argument: TEXT
-            description: Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine mean structure of "metric". [optional]
+            description: Input column name that has concentration information for the samples [optional]
           - names:
-              - --p-random-effects
+              - --p-prev-control-column
             argument: TEXT
-            description: Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine the variance and covariance structure (random effects) of "metric". To add a random slope, the same value passed to "state-column" should be passed here. A random intercept for each individual is set by default and does not need to be passed here. [optional]
+            description: Input column name containing experimental or control sample metadata [optional]
           - names:
-              - --p-palette
+              - --p-prev-control-indicator
             argument: TEXT
-            description: Color palette to use for generating boxplots.
+            description: indicate the control sample identifier (e.g. "control" or "blank") [optional]
           - names:
-              - --p-lowess
-              - --p-no-lowess
+              - --p-threshold
+            argument: NUMBER
+            description: 'Select threshold cutoff for decontam algorithm scores [default: 0.1]'
+          - names:
+              - --p-weighted
+              - --p-no-weighted
             argument: ""
-            description: 'Estimate locally weighted scatterplot smoothing. Note that this will eliminate confidence interval plotting. [default: False]'
+            description: 'weight the decontam scores by their associated read number [default: True]'
           - names:
-              - --p-ci
+              - --p-bin-size
             argument: NUMBER
-            description: Size of the confidence interval for the regression
+            description: 'Select bin size for the histogram [default: 0.02]'
           - names:
-              - --p-formula
-            argument: TEXT
-            description: R-style formula to use for model specification. A formula must be used if the "metric" parameter is None. Note that the metric and group columns specified in the formula will override metric and group columns that are passed separately as parameters to this method. Formulae will be in the format "a ~ b + c", where "a" is the metric (dependent variable) and "b" and "c" are independent covariates. Use "+" to add a variable; "+ a:b" to add an interaction between variables a and b; "*" to include a variable and all interactions; and "-" to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [optional]
+              - --o-batch-subset-tables
+            argument: ARTIFACTS... Collection[FeatureTable[Frequency]]
+            description: Directory where feature tables split based on metadata and parameter split-column values should be written. [required]
           - names:
-              - --o-visualization
+              - --o-decontam-scores
+            argument: ARTIFACTS... Collection[FeatureData[DecontamScore]]
+            description: The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence [required]
+          - names:
+              - --o-score-histograms
             argument: VISUALIZATION
-            description: '[required]'
+            description: The vizulaizer histograms for all decontam score objects generated from the pipeline [required]
           - names:
               - --output-dir
             argument: PATH
@@ -6911,6 +11705,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -6923,117 +11737,88 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: maturity-index
-        description: Microbial maturity index prediction.
-        usage: qiime longitudinal maturity-index [OPTIONS]
+      - name: decontam-remove
+        description: Remove contaminants
+        usage: qiime quality-control decontam-remove [OPTIONS]
         options:
+          - names:
+              - --i-decontam-scores
+            argument: ARTIFACT FeatureData[DecontamScore]
+            description: Pre-feature decontam scores. [required]
           - names:
               - --i-table
             argument: ARTIFACT FeatureTable[Frequency]
-            description: Feature table containing all features that should be used for target prediction. [required]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: metadata file(s) [required]
-          - names:
-              - --p-state-column
-            argument: TEXT
-            description: Numeric metadata column containing sampling time (state) data to use as prediction target. [required]
-          - names:
-              - --p-group-by
-            argument: TEXT
-            description: Categorical metadata column to use for plotting and significance testing between main treatment groups. [required]
-          - names:
-              - --p-control
-            argument: TEXT
-            description: Value of group-by to use as control group. The regression model will be trained using only control group data, and the maturity scores of other groups consequently will be assessed relative to this group. [required]
-          - names:
-              - --p-individual-id-column
-            argument: TEXT
-            description: Optional metadata column containing IDs for individual subjects. Adds individual subject (spaghetti) vectors to volatility charts if a column name is provided. [optional]
-          - names:
-              - --p-estimator
-            argument: '{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor[DecisionTree], AdaBoostRegressor[ExtraTrees], ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}'
-            description: Regression model to use for prediction.
-          - names:
-              - --p-n-estimators
-            argument: INTEGER
-            description: Number of trees to grow for estimation.
+            description: Feature table from which contaminants will be removed. [required]
           - names:
-              - --p-test-size
-            argument: PROPORTION
-            description: Fraction of input samples to exclude from training set and use for classifier testing.
+              - --i-rep-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Feature representative sequences from which contaminants will be removed. [required]
           - names:
-              - --p-step
-            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
-            description: If optimize-feature-selection is True, step is the percentage of features to remove at each iteration.
+              - --p-threshold
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: Decontam score threshold. Features with a score less than or equal to this threshold will be removed.
           - names:
-              - --p-cv
-            argument: INTEGER
-            description: Number of k-fold cross-validations to perform.
+              - --o-filtered-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Feature table with contaminants removed. [required]
           - names:
-              - --p-random-state
-            argument: INTEGER
-            description: Seed used by random number generator. [optional]
+              - --o-filtered-rep-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Feature representative sequences with contaminants removed. [required]
           - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'Number of jobs to run in parallel. [default: 1]'
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-parameter-tuning
-              - --p-no-parameter-tuning
+              - --verbose
+              - --quiet
             argument: ""
-            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-optimize-feature-selection
-              - --p-no-optimize-feature-selection
-            argument: ""
-            description: Automatically optimize input feature selection using recursive feature elimination.
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-stratify
-              - --p-no-stratify
+              - --citations
             argument: ""
-            description: 'Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: False]'
-          - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
-          - names:
-              - --p-feature-count
-            argument: INTEGER
-            description: Filter feature table to include top N most important features.
+            description: Show citations and exit.
           - names:
-              - --o-sample-estimator
-            argument: ARTIFACT SampleEstimator[Regressor]
-            description: Trained sample estimator. [required]
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: decontam-score-viz
+        description: Generate a histogram representation of the scores
+        usage: qiime quality-control decontam-score-viz [OPTIONS]
+        options:
           - names:
-              - --o-feature-importance
-            argument: ARTIFACT FeatureData[Importance]
-            description: Importance of each input feature to model accuracy. [required]
+              - --i-decontam-scores
+            argument: ARTIFACTS... Collection[FeatureData[DecontamScore]]
+            description: Output from decontam identify to be visualized
           - names:
-              - --o-predictions
-            argument: ARTIFACT SampleData[RegressorPredictions]
-            description: Predicted target values for each input sample. [required]
+              - --i-table
+            argument: ARTIFACTS... Collection[FeatureTable[Frequency]]
+            description: Raw OTU/ASV table that was used as input to decontam-identify [required]
           - names:
-              - --o-model-summary
-            argument: VISUALIZATION
-            description: Summarized parameter and (if enabled) feature selection information for the trained estimator. [required]
+              - --i-rep-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Representative Sequences table which contaminate sequences will be removed from [optional]
           - names:
-              - --o-accuracy-results
-            argument: VISUALIZATION
-            description: Accuracy results visualization. [required]
+              - --p-threshold
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: 'Select threshold cutoff for decontam algorithm scores [default: 0.1]'
           - names:
-              - --o-maz-scores
-            argument: ARTIFACT SampleData[RegressorPredictions]
-            description: Microbiota-for-age z-score predictions. [required]
+              - --p-weighted
+              - --p-no-weighted
+            argument: ""
+            description: 'weight the decontam scores by their associated read number [default: True]'
           - names:
-              - --o-clustermap
-            argument: VISUALIZATION
-            description: Heatmap of important feature abundance at each time point in each group. [required]
+              - --p-bin-size
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: 'Select bin size for the histogram [default: 0.02]'
           - names:
-              - --o-volatility-plots
+              - --o-visualization
             argument: VISUALIZATION
-            description: Interactive volatility plots of MAZ and maturity scores, target (column) predictions, and the sample metadata. [required]
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -7043,26 +11828,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -7075,34 +11840,71 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: nmit
-        description: Nonparametric microbial interdependence test
-        usage: qiime longitudinal nmit [OPTIONS]
+      - name: evaluate-composition
+        description: Evaluate expected vs. observed taxonomic composition of samples
+        usage: qiime quality-control evaluate-composition [OPTIONS]
         options:
           - names:
-              - --i-table
+              - --i-expected-features
             argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Feature table to use for microbial interdependence test. [required]
+            description: Expected feature compositions [required]
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata file containing individual-id-column. [required]
+              - --i-observed-features
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: Observed feature compositions [required]
           - names:
-              - --p-individual-id-column
-            argument: TEXT
-            description: Metadata column containing IDs for individual subjects. [required]
+              - --p-depth
+            argument: INTEGER
+            description: 'Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [default: 7]'
           - names:
-              - --p-corr-method
-            argument: TEXT Choices('kendall', 'pearson', 'spearman')
-            description: The temporal correlation test to be applied.
+              - --p-plot-tar
+              - --p-no-plot-tar
+            argument: ""
+            description: 'Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true positive features divided by the total number of observed features (TAR = true positives / (true positives + false positives)). [default: True]'
           - names:
-              - --p-dist-method
-            argument: TEXT Choices('fro', 'nuc')
-            description: 'Temporal distance method, see numpy.linalg.norm for details. [default: ''fro'']'
+              - --p-plot-tdr
+              - --p-no-plot-tdr
+            argument: ""
+            description: 'Plot taxon detection rate (TDR) on score plot. TDR is the number of true positive features divided by the total number of expected features (TDR = true positives / (true positives + false negatives)). [default: True]'
           - names:
-              - --o-distance-matrix
-            argument: ARTIFACT
-            description: DistanceMatrix The resulting distance matrix. [required]
+              - --p-plot-r-value
+              - --p-no-plot-r-value
+            argument: ""
+            description: 'Plot expected vs. observed linear regression r value on score plot. [default: False]'
+          - names:
+              - --p-plot-r-squared
+              - --p-no-plot-r-squared
+            argument: ""
+            description: 'Plot expected vs. observed linear regression r-squared value on score plot. [default: True]'
+          - names:
+              - --p-plot-bray-curtis
+              - --p-no-plot-bray-curtis
+            argument: ""
+            description: 'Plot expected vs. observed Bray-Curtis dissimilarity scores on score plot. [default: False]'
+          - names:
+              - --p-plot-jaccard
+              - --p-no-plot-jaccard
+            argument: ""
+            description: 'Plot expected vs. observed Jaccard distances scores on score plot. [default: False]'
+          - names:
+              - --p-plot-observed-features
+              - --p-no-plot-observed-features
+            argument: ""
+            description: Plot observed features count on score plot.
+          - names:
+              - --p-plot-observed-features-ratio
+              - --p-no-plot-observed-features-ratio
+            argument: ""
+            description: 'Plot ratio of observed:expected features on score plot. [default: True]'
+          - names:
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs. [optional]
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -7124,51 +11926,23 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: pairwise-differences
-        description: Paired difference testing and boxplots
-        usage: qiime longitudinal pairwise-differences [OPTIONS]
+      - name: evaluate-seqs
+        description: Compare query (observed) vs. reference (expected) sequences.
+        usage: qiime quality-control evaluate-seqs [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Feature table to optionally use for paired comparisons. [optional]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata file containing individual-id-column. [required]
-          - names:
-              - --p-metric
-            argument: TEXT
-            description: Numerical metadata or artifact column to test. [required]
-          - names:
-              - --p-state-column
-            argument: TEXT
-            description: Metadata column containing state (e.g., Time) across which samples are paired. [required]
-          - names:
-              - --p-state-1
-            argument: TEXT
-            description: Baseline state column value. [required]
-          - names:
-              - --p-state-2
-            argument: TEXT
-            description: State column value to pair with baseline. [required]
-          - names:
-              - --p-individual-id-column
-            argument: TEXT
-            description: 'Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling="random" to instead randomly select one member. [required]'
+              - --i-query-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences to test for exclusion [required]
           - names:
-              - --p-group-column
-            argument: TEXT
-            description: Metadata column on which to separate groups for comparison [optional]
+              - --i-reference-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Reference sequences to align against feature sequences
           - names:
-              - --p-parametric
-              - --p-no-parametric
+              - --p-show-alignments
+              - --p-no-show-alignments
             argument: ""
-            description: Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
-          - names:
-              - --p-replicate-handling
-            argument: TEXT Choices('error', 'random', 'drop')
-            description: 'Choose how replicate samples are handled. If replicates are detected, "error" causes method to fail; "drop" will discard all replicated samples; "random" chooses one representative at random from among replicates. [default: ''error'']'
+            description: 'Option to plot pairwise alignments of query sequences and their top hits. [default: False]'
           - names:
               - --o-visualization
             argument: VISUALIZATION
@@ -7194,47 +11968,40 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: pairwise-distances
-        description: Paired pairwise distance testing and boxplots
-        usage: qiime longitudinal pairwise-distances [OPTIONS]
+      - name: evaluate-taxonomy
+        description: Evaluate expected vs. observed taxonomic assignments
+        usage: qiime quality-control evaluate-taxonomy [OPTIONS]
         options:
           - names:
-              - --i-distance-matrix
-            argument: ARTIFACT
-            description: Matrix of distances between pairs of samples. [required]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata file containing individual-id-column. [required]
-          - names:
-              - --p-group-column
-            argument: TEXT
-            description: Metadata column on which to separate groups for comparison [required]
+              - --i-expected-taxa
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Expected taxonomic assignments [required]
           - names:
-              - --p-state-column
-            argument: TEXT
-            description: Metadata column containing state (e.g., Time) across which samples are paired. [required]
+              - --i-observed-taxa
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Observed taxonomic assignments [required]
           - names:
-              - --p-state-1
-            argument: TEXT
-            description: Baseline state column value. [required]
+              - --i-feature-table
+            argument: ARTIFACT FeatureTable[RelativeFrequency]
+            description: Optional feature table containing relative frequency of each feature, used to weight accuracy scores by frequency. Must contain all features found in expected and/or observed taxa. Features found in the table but not the expected/observed taxa will be dropped prior to analysis. [optional]
           - names:
-              - --p-state-2
-            argument: TEXT
-            description: State column value to pair with baseline. [required]
+              - --p-depth
+            argument: INTEGER
+            description: Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [required]
           - names:
-              - --p-individual-id-column
-            argument: TEXT
-            description: 'Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling="random" to instead randomly select one member. [required]'
+              - --p-require-exp-ids
+              - --p-no-require-exp-ids
+            argument: ""
+            description: Require that all features found in observed taxa must be found in expected taxa or raise error.
           - names:
-              - --p-parametric
-              - --p-no-parametric
+              - --p-require-obs-ids
+              - --p-no-require-obs-ids
             argument: ""
-            description: Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
+            description: Require that all features found in expected taxa must be found in observed taxa or raise error.
           - names:
-              - --p-replicate-handling
-            argument: TEXT Choices('error', 'random', 'drop')
-            description: 'Choose how replicate samples are handled. If replicates are detected, "error" causes method to fail; "drop" will discard all replicated samples; "random" chooses one representative at random from among replicates. [default: ''error'']'
+              - --p-sample-id
+            argument: TEXT
+            description: Optional sample ID to use for extracting frequency data from feature table, and for labeling accuracy results. If no sample-id is provided, feature frequencies are derived from the sum of all samples present in the feature table. [optional]
           - names:
               - --o-visualization
             argument: VISUALIZATION
@@ -7260,50 +12027,42 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: plot-feature-volatility
-        description: Plot longitudinal feature volatility and importances
-        usage: qiime longitudinal plot-feature-volatility [OPTIONS]
+      - name: exclude-seqs
+        description: Exclude sequences by alignment
+        usage: qiime quality-control exclude-seqs [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Feature table containing features found in importances. [required]
-          - names:
-              - --i-importances
-            argument: ARTIFACT FeatureData[Importance]
-            description: Feature importance scores. [required]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata file containing individual-id-column. [required]
-          - names:
-              - --p-state-column
-            argument: TEXT
-            description: Metadata column containing state (time) variable information. [required]
+              - --i-query-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences to test for exclusion [required]
           - names:
-              - --p-individual-id-column
-            argument: TEXT
-            description: Metadata column containing IDs for individual subjects. [optional]
+              - --i-reference-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Reference sequences to align against feature sequences [required]
           - names:
-              - --p-default-group-column
-            argument: TEXT
-            description: The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization).
+              - --p-perc-identity
+            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
+            description: 'Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0] [default: 0.97]'
           - names:
-              - --p-yscale
-            argument: TEXT Choices('linear', 'pow', 'sqrt', 'log')
-            description: 'y-axis scaling strategy to apply. [default: ''linear'']'
+              - --p-evalue
+            argument: NUMBER
+            description: BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default. [optional]
           - names:
-              - --p-importance-threshold
-            argument: VALUE
-            description: Filter feature table to exclude any features with an importance score less than this threshold.
+              - --p-perc-query-aligned
+            argument: NUMBER
+            description: Percent of query sequence that must align to reference in order to be accepted as a hit.
           - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+              - --p-threads
+            argument: NTHREADS
+            description: 'Number of threads to use. Only applies to vsearch method. [default: 1]'
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-sequence-hits
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Subset of feature sequences that align to reference sequences [required]
+          - names:
+              - --o-sequence-misses
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Subset of feature sequences that do not align to reference sequences [required]
           - names:
               - --output-dir
             argument: PATH
@@ -7325,42 +12084,35 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: volatility
-        description: Generate interactive volatility plot
-        usage: qiime longitudinal volatility [OPTIONS]
+      - name: filter-reads
+        description: Filter demultiplexed sequences by alignment to reference database.
+        usage: qiime quality-control filter-reads [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Feature table containing metrics. [optional]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Sample metadata file containing individual-id-column. [required]
-          - names:
-              - --p-state-column
-            argument: TEXT
-            description: Metadata column containing state (time) variable information. [required]
+              - --i-database
+            argument: ARTIFACT
+            description: Bowtie2 indexed database.
           - names:
-              - --p-individual-id-column
-            argument: TEXT
-            description: Metadata column containing IDs for individual subjects. [optional]
+              - --p-n-threads
+            argument: NTHREADS
+            description: 'Number of alignment threads to launch. [default: 1]'
           - names:
-              - --p-default-group-column
-            argument: TEXT
-            description: The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization).
+              - --p-mode
+            argument: TEXT Choices('local', 'global')
+            description: 'Bowtie2 alignment settings. See bowtie2 manual for more details. [default: ''local'']'
           - names:
-              - --p-default-metric
-            argument: TEXT
-            description: Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization). [optional]
+              - --p-ref-gap-open-penalty
+            argument: ""
+            description: INTEGER
           - names:
-              - --p-yscale
-            argument: TEXT Choices('linear', 'pow', 'sqrt', 'log')
-            description: 'y-axis scaling strategy to apply. [default: ''linear'']'
+              - --p-ref-gap-ext-penalty
+            argument: ""
+            description: INTEGER
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --p-exclude-seqs
+              - --p-no-exclude-seqs
+            argument: ""
+            description: 'Exclude sequences that align to reference. Set this option to False to exclude sequences that do not align to the reference database. [default: True]'
           - names:
               - --output-dir
             argument: PATH
@@ -7382,9 +12134,29 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: metadata
-    description: Plugin for working with Metadata.
-    usage: qiime metadata [OPTIONS] COMMAND [ARGS]...
+  - name: quality-filter
+    description: Plugin for PHRED-based filtering and trimming.
+    usage: qiime quality-filter [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+  - name: rescript
+    description: Pipeline for reference sequence annotation and curation.
+    usage: qiime rescript [OPTIONS] COMMAND [ARGS]...
     options:
       - names:
           - --version
@@ -7403,19 +12175,30 @@ subcommands:
         argument: ""
         description: Show this message and exit.
     subcommands:
-      - name: distance-matrix
-        description: Create a distance matrix from a numeric Metadata column
-        usage: qiime metadata distance-matrix [OPTIONS]
+      - name: cull-seqs
+        description: Removes sequences that contain at least the specified number of degenerate bases and/or homopolymers of a given length.
+        usage: qiime rescript cull-seqs [OPTIONS]
         options:
           - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Numeric metadata column to compute pairwise Euclidean distances from [required]
+              - --i-sequences
+            argument: ARTIFACT FeatureData[Sequence | RNASequence]
+            description: DNA or RNA Sequences to be screened for removal based on degenerate base and homopolymer screening criteria. [required]
           - names:
-              - --o-distance-matrix
-            argument: ARTIFACT
-            description: DistanceMatrix [required]
+              - --p-num-degenerates
+            argument: INTEGER
+            description: Sequences with N, or more, degenerate bases will be removed.
+          - names:
+              - --p-homopolymer-length
+            argument: INTEGER
+            description: Sequences containing a homopolymer sequence of length N, or greater, will be removed.
+          - names:
+              - --p-n-jobs
+            argument: INTEGER
+            description: Number of concurrent processes to use while processing sequences.
+          - names:
+              - --o-clean-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The resulting DNA sequences that pass degenerate base and homopolymer screening criteria. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -7437,22 +12220,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: merge
-        description: Merge metadata
-        usage: qiime metadata merge [OPTIONS]
+      - name: degap-seqs
+        description: Remove gaps from DNA sequence alignments.
+        usage: qiime rescript degap-seqs [OPTIONS]
         options:
           - names:
-              - --m-metadata1-file
-            argument: METADATA...
-            description: First metadata file to merge. [required]
+              - --i-aligned-sequences
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: Aligned DNA Sequences to be degapped. [required]
           - names:
-              - --m-metadata2-file
-            argument: METADATA...
-            description: Second metadata file to merge. [required]
+              - --p-min-length
+            argument: INTEGER
+            description: 'Minimum length of sequence to be returned after degapping. [default: 1]'
           - names:
-              - --o-merged-metadata
-            argument: ARTIFACT
-            description: ImmutableMetadata The merged metadata. [required]
+              - --o-degapped-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: The resulting unaligned (degapped) DNA sequences.
           - names:
               - --output-dir
             argument: PATH
@@ -7474,36 +12257,97 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: shuffle-groups
-        description: Shuffle values in a categorical sample metadata column.
-        usage: qiime metadata shuffle-groups [OPTIONS]
+      - name: dereplicate
+        description: Dereplicate features with matching sequences and taxonomies.
+        usage: qiime rescript dereplicate [OPTIONS]
         options:
           - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Categorical metadata column to shuffle. [required]
+              - --i-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences to be dereplicated [required]
           - names:
-              - --p-n-columns
+              - --i-taxa
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomic classifications of sequences to be dereplicated [required]
+          - names:
+              - --p-mode
+            argument: TEXT Choices('uniq', 'lca', 'majority', 'super')
+            description: How to handle dereplication when sequences map to distinct taxonomies. "uniq" will retain all sequences with unique taxonomic affiliations. "lca" will find the least common ancestor among all taxa sharing a sequence. "majority" will find the most common taxonomic label associated with that sequence; note that in the event of a tie, "majority" will pick the winner arbitrarily. "super" finds the LCA consensus while giving preference to majority labels and collapsing substrings into superstrings. For example, when a more specific taxonomy does not contradict a less specific taxonomy, the more specific is chosen. That is, "g__Faecalibacterium; s__prausnitzii", will be preferred over "g__Faecalibacterium; s__"
+          - names:
+              - --p-threads
             argument: INTEGER
-            description: The number of shuffled metadata columns to create.
+            description: Number of computation threads to use (1 to 256).
           - names:
-              - --p-md-column-name-prefix
-            argument: TEXT
-            description: 'Prefix to use in naming the shuffled metadata columns. [default: ''shuffled.grouping.'']'
+              - --p-rank-handles
+            argument: VALUES...
+            description: Specifies the set of rank handles used to backfill missing ranks in the resulting dereplicated taxonomy.
           - names:
-              - --p-md-column-values-prefix
-            argument: TEXT
-            description: 'Prefix to use in naming the values in the shuffled metadata columns. [default: ''fake.group.'']'
+              - --p-derep-prefix
+              - --p-no-derep-prefix
+            argument: ""
+            description: 'Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False]'
           - names:
-              - --p-encode-sample-size
-              - --p-no-encode-sample-size
+              - --o-dereplicated-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: '[required]'
+          - names:
+              - --o-dereplicated-taxa
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
             argument: ""
-            description: If true, the sample size of each metadata group will be appended to the shuffled metadata column values.
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: edit-taxonomy
+        description: Edit taxonomy strings with find and replace terms.
+        usage: qiime rescript edit-taxonomy [OPTIONS]
+        options:
+          - names:
+              - --i-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomy strings data to be edited. [required]
+          - names:
+              - --m-replacement-map-file
+            argument: ""
+            description: METADATA
+          - names:
+              - --m-replacement-map-column
+            argument: COLUMN  MetadataColumn[Categorical]
+            description: A tab-delimitad metadata file in which the strings in the 'id' column are replaced by the 'replacement-strings' in the second column. All strings in the 'id' column must be unique! [optional]
+          - names:
+              - --p-search-strings
+            argument: TEXT...
+            description: Only used in conjuntion with 'replacement-strings'.
+          - names:
+              - --p-replacement-strings
+            argument: TEXT...
+            description: Only used in conjuntion with 'search-strings'.
+          - names:
+              - --p-use-regex
+              - --p-no-use-regex
+            argument: ""
+            description: Toggle regular expressions. By default, only litereal substring matching is performed.
           - names:
-              - --o-shuffled-groups
-            argument: ARTIFACT SampleData[ArtificialGrouping]
-            description: Randomized metadata columns [required]
+              - --o-edited-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomy in which the original strings are replaced by user-supplied strings. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -7525,22 +12369,26 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: tabulate
-        description: Interactively explore Metadata in an HTML table
-        usage: qiime metadata tabulate [OPTIONS]
+      - name: evaluate-classifications
+        description: Interactively evaluate taxonomic classification accuracy.
+        usage: qiime rescript evaluate-classifications [OPTIONS]
         options:
           - names:
-            - --m-input-file
-            argument: METADATA...
-            description: The metadata to tabulate. [required]
+              - --i-expected-taxonomies
+            argument: ARTIFACTS... List[FeatureData[Taxonomy]]
+            description: True taxonomic labels for one more more sets of features. [required]
           - names:
-              - --p-page-size
-            argument: INTEGER
-            description: 'The maximum number of Metadata records to display per page [default: 100]'
+              - --i-observed-taxonomies
+            argument: ARTIFACTS... List[FeatureData[Taxonomy]]
+            description: Predicted classifications of same sets of features, input in same order as expected-taxonomies.
           - names:
-              - --o-visualization
+              - --p-labels
+            argument: TEXT...
+            description: List of labels to use for labeling evaluation
+          - names:
+              - --o-evaluation
             argument: VISUALIZATION
-            description: '[required]'
+            description: Visualization of classification accuracy results.
           - names:
               - --output-dir
             argument: PATH
@@ -7550,6 +12398,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -7562,68 +12430,50 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: phylogeny
-    description: Plugin for generating and manipulating phylogenies.
-    usage: qiime phylogeny [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: align-to-tree-mafft-fasttree
-        description: Build a phylogenetic tree using fasttree and
-        usage: qiime phylogeny align-to-tree-mafft-fasttree [OPTIONS]
+      - name: evaluate-cross-validate
+        description: Evaluate DNA sequence reference database via cross-validated taxonomic classification.
+        usage: qiime rescript evaluate-cross-validate [OPTIONS]
         options:
           - names:
               - --i-sequences
             argument: ARTIFACT FeatureData[Sequence]
-            description: The sequences to be used for creating a fasttree based rooted phylogenetic tree. [required]
+            description: Reference sequences to use for classifier training/testing. [required]
           - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'The number of threads. (Use `auto` to automatically use all available cores) This value is used when aligning the sequences and creating the tree with fasttree. [default: 1]'
+              - --i-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Reference taxonomy to use for classifier training/testing. [required]
           - names:
-              - --p-mask-max-gap-frequency
-            argument: PROPORTION Range(0, 1, inclusive_end=True)
-            description: The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences.
+              - --p-k
+            argument: INTEGER
+            description: Number of stratified folds.
           - names:
-              - --p-mask-min-conservation
-            argument: PROPORTION Range(0, 1, inclusive_end=True)
-            description: The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences.
+              - --p-random-state
+            argument: INTEGER
+            description: Seed used by the random number generator.
           - names:
-              - --p-parttree
-              - --p-no-parttree
-            argument: ""
-            description: 'This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. [default: False]'
+              - --p-reads-per-batch
+            argument: VALUE
+            description: Number of reads to process in each batch. If "auto", this parameter is autoscaled to min( number of query sequences / n-jobs, 20000).
           - names:
-              - --o-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: The aligned sequences. [required]
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]'
           - names:
-              - --o-masked-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: The masked alignment. [required]
+              - --p-confidence
+            argument: VALUE
+            description: Confidence threshold for limiting taxonomic depth.
           - names:
-              - --o-tree
-            argument: ARTIFACT
-            description: The unrooted phylogenetic tree.
+              - --o-expected-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Expected taxonomic label for each input sequence. Taxonomic labels may be truncated due to k-fold CV and stratification. [required]
           - names:
-              - --o-rooted-tree
-            argument: ARTIFACT
-            description: Phylogeny[Rooted] The rooted phylogenetic tree. [required]
+              - --o-observed-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Observed taxonomic label for each input sequence, predicted by cross-validation. [required]
+          - names:
+              - --o-evaluation
+            argument: VISUALIZATION
+            description: Visualization of cross-validated accuracy results. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -7665,67 +12515,42 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: align-to-tree-mafft-iqtree
-        description: Build a phylogenetic tree using iqtree and
-        usage: qiime phylogeny align-to-tree-mafft-iqtree [OPTIONS]
+      - name: evaluate-fit-classifier
+        description: Evaluate and train naive Bayes classifier on reference sequences.
+        usage: qiime rescript evaluate-fit-classifier [OPTIONS]
         options:
           - names:
               - --i-sequences
             argument: ARTIFACT FeatureData[Sequence]
-            description: The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]
-          - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: The number of threads. (Use 0 to automatically use all available cores This value is used when aligning the sequences and creating the tree with iqtree.
-          - names:
-              - --p-mask-max-gap-frequency
-            argument: PROPORTION Range(0, 1, inclusive_end=True)
-            description: The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences.
-          - names:
-              - --p-mask-min-conservation
-            argument: PROPORTION Range(0, 1, inclusive_end=True)
-            description: The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences.
-          - names:
-              - --p-substitution-model
-            argument: TEXT
-            description: Model of Nucleotide Substitution. If not provided, IQ-TREE will determine the best fit substitution model automatically.
-          - names:
-              - --p-fast
-              - --p-no-fast
-            argument: ""
-            description: 'Fast search to resemble FastTree. [default: False]'
-          - names:
-              - --p-alrt
-            argument: INTEGER
-            description: Single branch test method. Number of bootstrap replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is required.
-          - names:
-              - --p-stop-iter
-            argument: INTEGER
-            description: Number of unsuccessful iterations to stop. If not set, program defaults will be used.
+            description: Reference sequences to use for classifier training/testing. [required]
           - names:
-              - --p-perturb-nni-strength
-            argument: NUMBER
-            description: Perturbation strength for randomized NNI.
+              - --i-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Reference taxonomy to use for classifier training/testing. [required]
           - names:
-              - --p-seed
-            argument: INTEGER
-            description: Random number seed for the iqtree parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]
+              - --p-reads-per-batch
+            argument: VALUE
+            description: Number of reads to process in each batch. If "auto", this parameter is autoscaled to min( number of query sequences / n-jobs, 20000).
           - names:
-              - --o-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: The aligned sequences. [required]
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]'
           - names:
-              - --o-masked-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: The masked alignment. [required]
+              - --p-confidence
+            argument: VALUE
+            description: Confidence threshold for limiting taxonomic depth.
           - names:
-              - --o-tree
+              - --o-classifier
             argument: ARTIFACT
-            description: The unrooted phylogenetic tree.
+            description: Trained naive Bayes taxonomic classifier. [required]
           - names:
-              - --o-rooted-tree
-            argument: ARTIFACT
-            description: Phylogeny[Rooted] The rooted phylogenetic tree. [required]
+              - --o-evaluation
+            argument: VISUALIZATION
+            description: Visualization of classification accuracy results. [required]
+          - names:
+              - --o-observed-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Observed taxonomic label for each input sequence, predicted by the trained classifier. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -7748,13 +12573,62 @@ subcommands:
             argument: ""
             description: Execute your action in parallel. This flag will use your default parallel config.
           - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+          - names:
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
+            argument: ""
+            description: Show citations and exit.
+          - names:
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: evaluate-seqs
+        description: Compute summary statistics on sequence artifact(s).
+        usage: qiime rescript evaluate-seqs [OPTIONS]
+        options:
+          - names:
+              - --i-sequences
+            argument: ARTIFACTS... List[FeatureData[Sequence]]
+            description: One or more sets of sequences to evaluate. [required]
+          - names:
+              - --p-labels
+            argument: TEXT...
+            description: List of labels to use for labeling evaluation results in the resulting visualization.
+          - names:
+              - --p-kmer-lengths
+            argument: INTEGERS...
+            description: Sequence kmer lengths to optionally use for entropy calculation.
+          - names:
+              - --p-subsample-kmers
+            argument: PROPORTION
+            description: Optionally subsample sequences prior to kmer entropy measurement.
+          - names:
+              - --p-palette
+            argument: TEXT
+            description: Color palette to use for plotting evaluation results.
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
               - --example-data
             argument: PATH
@@ -7767,55 +12641,26 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: align-to-tree-mafft-raxml
-        description: Build a phylogenetic tree using raxml and
-        usage: qiime phylogeny align-to-tree-mafft-raxml [OPTIONS]
+      - name: evaluate-taxonomy
+        description: Compute summary statistics on taxonomy artifact(s).
+        usage: qiime rescript evaluate-taxonomy [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]
-          - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'The number of threads. (Use `all` to automatically use all available cores. This value is used when aligning the sequences and creating the tree with iqtree. [default: 1]'
-          - names:
-              - --p-mask-max-gap-frequency
-            argument: PROPORTION Range(0, 1, inclusive_end=True)
-            description: The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences.
-          - names:
-              - --p-mask-min-conservation
-            argument: PROPORTION Range(0, 1, inclusive_end=True)
-            description: The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences.
-          - names:
-              - --p-parttree
-              - --p-no-parttree
-            argument: ""
-            description: 'This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. NOTE: if using this option, it is recomended that only the CAT-based substitution models of RAxML be considered for this pipeline.'
-          - names:
-              - --p-seed
-            argument: INTEGER
-            description: Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen.
-          - names:
-              - --p-raxml-version
-            argument: TEXT Choices('Standard', 'SSE3', 'AVX2')
-            description: Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version.
-          - names:
-              - --o-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: The aligned sequences. [required]
+              - --i-taxonomies
+            argument: ARTIFACTS... List[FeatureData[Taxonomy]]
+            description: One or more taxonomies to evaluate. [required]
           - names:
-              - --o-masked-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: The masked alignment. [required]
+              - --p-labels
+            argument: TEXT...
+            description: List of labels to use for labeling evaluation results in the resulting visualization.
           - names:
-              - --o-tree
-            argument: ARTIFACT
-            description: The unrooted phylogenetic tree.
+              - --p-rank-handle-regex
+            argument: TEXT
+            description: Regular expression indicating which taxonomic rank a label belongs to; this handle is stripped from the label prior to operating on the taxonomy. The net effect is that ambiguous or empty levels can be removed prior to comparison, enabling selection of taxonomies with more complete taxonomic information. For example, "^[dkpcofgs]__" will recognize greengenes or silva rank handles. [optional]
           - names:
-              - --o-rooted-tree
-            argument: ARTIFACT
-            description: Phylogeny[Rooted] The rooted phylogenetic tree. [required]
+              - --o-taxonomy-stats
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -7857,22 +12702,38 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: fasttree
-        description: Construct a phylogenetic tree with FastTree.
-        usage: qiime phylogeny fasttree [OPTIONS]
+      - name: extract-seq-segments
+        description: Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value.
+        usage: qiime rescript extract-seq-segments [OPTIONS]
         options:
           - names:
-              - --i-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: Aligned sequences to be used for phylogenetic reconstruction. [required]
+              - --i-input-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences from which matching shorter sequence segments (regions) can be extracted from. Sequences containing segments that match those from 'reference-segment-sequences' will have those segments extracted and written to file. [required]
           - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'The number of threads. Using more than one thread runs the non-deterministic variant of `FastTree` (`FastTreeMP`), and may result in a different tree than single-threading. See http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto` to automatically use all available cores) [default: 1]'
+              - --i-reference-segment-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Reference sequence segments that will be used to search for and extract matching segments from 'sequences'. [required]
           - names:
-              - --o-tree
-            argument: ARTIFACT
-            description: The resulting phylogenetic tree.
+              - --p-perc-identity
+            argument: PROPORTION
+            description: The percent identity at which clustering should be performed.
+          - names:
+              - --p-min-seq-len
+            argument: INTEGER
+            description: Minimum length of sequence allowed for searching.
+          - names:
+              - --p-threads
+            argument: INTEGER
+            description: Number of computation threads to use (1 to 256).
+          - names:
+              - --o-extracted-sequence-segments
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Extracted sequence segments from 'input-sequences' that succesfully aligned to 'reference-segment-sequences'. [required]
+          - names:
+              - --o-unmatched-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences in 'input-sequences' that did not have matching sequence segments within 'reference-segment-sequences'. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -7894,18 +12755,34 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-table
-        description: Remove features from table if they're not
-        usage: qiime phylogeny filter-table [OPTIONS]
+      - name: filter-seqs-length
+        description: Filter sequences by length.
+        usage: qiime rescript filter-seqs-length [OPTIONS]
         options:
           - names:
-              - --i-tree
-            argument: ARTIFACT Phylogeny[Rooted | Unrooted]
-            description: Tree where tip identifiers are the feature identifiers that should be retained in the table. [required]
+              - --i-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences to be filtered by length. [required]
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable
-            description: Feature table that features should be filtered from.
+              - --p-global-min
+            argument: INTEGER
+            description: The minimum length threshold for filtering all sequences.
+          - names:
+              - --p-global-max
+            argument: INTEGER
+            description: The maximum length threshold for filtering all sequences.
+          - names:
+              - --p-threads
+            argument: INTEGER
+            description: Number of computation threads to use (1 to 256).
+          - names:
+              - --o-filtered-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences that pass the filtering thresholds.
+          - names:
+              - --o-discarded-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences that fall outside the filtering thresholds. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -7927,30 +12804,46 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-tree
-        description: Remove features from tree based on metadata
-        usage: qiime phylogeny filter-tree [OPTIONS]
+      - name: filter-seqs-length-by-taxon
+        description: Filter sequences by length and taxonomic group.
+        usage: qiime rescript filter-seqs-length-by-taxon [OPTIONS]
         options:
           - names:
-              - --i-tree
-            argument: ARTIFACT Phylogeny[Rooted¹ | Unrooted²]
-            description: Tree that should be filtered [required]
+              - --i-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences to be filtered by length. [required]
           - names:
-              -  --i-table
-            argument: ARTIFACT
-            description: Feature table which contains the identifier that should be retained in the tree
+              - --i-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomic classifications of sequences to be filtered. [required]
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: Feature metadata to use with the 'where' statement or to select tips to be retained.
+              - --p-labels
+            argument: TEXT...
+            description: One or more taxonomic labels to use for conditional filtering. [required]
           - names:
-              - --p-where
-            argument: TEXT
-            description: SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. [optional]
+              - --p-min-lens
+            argument: INTEGERS...
+            description: Minimum length thresholds to use for filtering sequences associated with each label.
           - names:
-              - --o-filtered-tree
-            argument: ARTIFACT Phylogeny[Rooted¹ | Unrooted²]
-            description: The resulting phylogenetic tree. [required]
+              - --p-max-lens
+            argument: INTEGERS...
+            description: Maximum length thresholds to use for filtering sequences associated with each label.
+          - names:
+              - --p-global-min
+            argument: INTEGER
+            description: The minimum length threshold for filtering all sequences.
+          - names:
+              - --p-global-max
+            argument: INTEGER
+            description: The maximum length threshold for filtering all sequences.
+          - names:
+              - --o-filtered-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences that pass the filtering thresholds.
+          - names:
+              - --o-discarded-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences that fall outside the filtering thresholds. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -7972,94 +12865,75 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: iqtree
-        description: Construct a phylogenetic tree with IQ-TREE.
-        usage: qiime phylogeny iqtree [OPTIONS]
+      - name: filter-taxa
+        description: Filter taxonomy by list of IDs or search criteria.
+        usage: qiime rescript filter-taxa [OPTIONS]
         options:
           - names:
-              - --i-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: Aligned sequences to be used for phylogenetic reconstruction. [required]
-          - names:
-              - --p-seed
-            argument: INTEGER
-            description: Random number seed. If not set, program defaults
-          - names:
-              - --p-n-cores
-            argument: NTHREADS
-            description: The number of cores to use for parallel processing.
-          - names:
-              - --p-n-cores-max
-            argument: NTHREADS
-            description: Limits the maximum number of cores to be used when
-          - names:
-              - --p-n-runs
-            argument: INTEGER
-            description: Number of indepedent runs. Multiple independent
-          - names:
-              - --p-substitution-model
-            argument: TEXT
-            description: Model of Nucleotide Substitution.
+              - --i-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomy to filter. [required]
           - names:
-              - --p-n-init-pars-trees
-            argument: INTEGER
-            description: Number of initial parsimony trees.
+              - --m-ids-to-keep-file
+            argument: METADATA...
+            description: List of IDs to keep (as Metadata).
           - names:
-              - --p-n-top-init-trees
-            argument: INTEGER
-            description: Number of top initial trees.
+              - --p-include
+            argument: TEXT...
+            description: List of search terms. Taxa containing one or more of these terms will be retained.
           - names:
-              - --p-n-best-retain-trees
-            argument: INTEGER
-            description: Number of best trees retained during search.
+              - --p-exclude
+            argument: TEXT...
+            description: List of search terms. Taxa containing one or more of these terms will be excluded.
           - names:
-              - --p-n-iter
-            argument: INTEGER
-            description: Fix number of iterations to stop.
+              - --o-filtered-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: The filtered taxonomy. [required]
           - names:
-              - --p-stop-iter
-            argument: INTEGER
-            description: Number of unsuccessful iterations to stop.
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-perturb-nni-strength
-            argument: NUMBER
-            description: Perturbation strength for randomized NNI.
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-spr-radius
-            argument: INTEGER
-            description: Radius for parsimony SPR search.
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-allnni
-              - --p-no-allnni
+              - --citations
             argument: ""
-            description: 'Perform more thorough NNI search. [default: False]'
+            description: Show citations and exit.
           - names:
-              - --p-fast
-              - --p-no-fast
+              - --help
             argument: ""
-            description: 'Fast search to resemble FastTree. [default: False]'
+            description: Show this message and exit.
+      - name: get-gtdb-data
+        description: Download, parse, and import SSU GTDB reference data.
+        usage: qiime rescript get-gtdb-data [OPTIONS]
+        options:
           - names:
-              - --p-alrt
-            argument: INTEGER
-            description: Single branch test method. Number of bootstrap
+              - --p-version
+            argument: TEXT Choices('202.0', '207.0', '214.0', '214.1')
+            description: 'GTDB database version to download. [default: ''214.1'']'
           - names:
-              - --p-abayes
-              - --p-no-abayes
-            argument: ""
-            description: Single branch test method. Approximate Bayes test.
+              - --p-domain
+            argument: TEXT Choices('Both', 'Bacteria', 'Archaea')
+            description: 'SSU sequence and taxonomy data to download from a given microbial domain from GTDB. ''Both'' will fetch both bacterial and archaeal data. ''Bacteria'' will only fetch bacterial data. ''Archaea'' will only fetch archaeal data. This only applies to ''db-type SpeciesReps''. [default: ''Both'']'
           - names:
-              - --p-lbp
-            argument: INTEGER
-            description: Single branch test method. Number of bootstrap
+              - --p-db-type
+            argument: TEXT Choices('All', 'SpeciesReps')
+            description: '''All'': All SSU data that pass the quality-control of GTDB, but are not clustered into representative species. ''SpeciesReps'': SSU gene sequences identified within the set of representative species. Note: if ''All'' is used, the ''domain'' parameter will be ignored as GTDB does not maintain separate domain-level files for these non-clustered data. [default: ''SpeciesReps'']'
           - names:
-              - --p-safe
-              - --p-no-safe
-            argument: ""
-            description: Safe likelihood kernel to avoid numerical
+              - --o-gtdb-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: SSU GTDB reference taxonomy. [required]
           - names:
-              - --o-tree
-            argument: ARTIFACT
-            description: The resulting phylogenetic tree.
+              - --o-gtdb-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: SSU GTDB reference sequences. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -8081,110 +12955,97 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: iqtree-ultrafast-bootstrap
-        description: Construct a phylogenetic tree with IQ-TREE
-        usage: qiime phylogeny iqtree-ultrafast-bootstrap [OPTIONS]
+      - name: get-ncbi-data
+        description: Download, parse, and import NCBI sequences and taxonomies
+        usage: qiime rescript get-ncbi-data [OPTIONS]
         options:
           - names:
-              - --i-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: Aligned sequences to be used for phylogenetic reconstruction. [required]
-          - names:
-              - --p-seed
-            argument: INTEGER
-            description: Random number seed. If not set, program defaults
-          - names:
-              - --p-n-cores
-            argument: NTHREADS
-            description: The number of cores to use for parallel processing.
-          - names:
-              - --p-n-cores-max
-            argument: NTHREADS
-            description: Limits the maximum number of cores to be used when
-          - names:
-              - --p-n-runs
-            argument: INTEGER
-            description: Number of indepedent runs. Multiple independent
-          - names:
-              - --p-substitution-model
+              - --p-query
             argument: TEXT
-            description: Model of Nucleotide Substitution.
+            description: Query on the NCBI Nucleotide database [optional]
           - names:
-              - --p-bootstrap-replicates
-            argument: INTEGER
-            description: The number of bootstrap searches to perform.
+              - --m-accession-ids-file
+            argument: METADATA...
+            description: List of accession ids for sequences in the NCBI Nucleotide database.
           - names:
-              - --p-n-init-pars-trees
-            argument: INTEGER
-            description: Number of initial parsimony trees.
+              - --p-ranks
+            argument: TEXT...
+            description: List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy database.
           - names:
-              - --p-n-top-init-trees
-            argument: INTEGER
-            description: Number of top initial trees.
+              - --p-rank-propagation
+              - --p-no-rank-propagation
+            argument: ""
+            description: Propagate known ranks to missing ranks if true
           - names:
-              - --p-n-best-retain-trees
-            argument: INTEGER
-            description: Number of best trees retained during search.
+              - --p-logging-level
+            argument: TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL')
+            description: Logging level
           - names:
-              - --p-stop-iter
+              - --p-n-jobs
             argument: INTEGER
-            description: Number of unsuccessful iterations to stop.
+            description: 'Number of concurrent download connections. More is faster until you run out of bandwidth. [default: 1]'
           - names:
-              - --p-perturb-nni-strength
-            argument: NUMBER
-            description: Perturbation strength for randomized NNI.
+              - --o-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Sequences from the NCBI Nucleotide database [required]
           - names:
-              - --p-spr-radius
-            argument: INTEGER
-            description: Radius for parsimony SPR search.
+              - --o-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomies from the NCBI Taxonomy database [required]
           - names:
-              - --p-n-max-ufboot-iter
-            argument: INTEGER
-            description: Maximum number of iterations.
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-n-ufboot-steps
-            argument: INTEGER
-            description: Number of iterations for UFBoot stopping rule.
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-min-cor-ufboot
-            argument: NUMBER
-            description: Minimum correlation coefficient.
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-ep-break-ufboot
-            argument: NUMBER
-            description: Epsilon value to break tie.
+              - --citations
+            argument: ""
+            description: Show citations and exit.
           - names:
-              - --p-allnni
-              - --p-no-allnni
+              - --help
             argument: ""
-            description: 'Perform more thorough NNI search. [default: False]'
+            description: Show this message and exit.
+      - name: get-ncbi-data-protein
+        description: Download, parse, and import NCBI protein sequences and taxonomies
+        usage: qiime rescript get-ncbi-data-protein [OPTIONS]
+        options:
           - names:
-              - --p-alrt
-            argument: INTEGER
-            description: Single branch test method.
+              - --p-query
+            argument: TEXT
+            description: Query on the NCBI Protein database [optional]
           - names:
-              - --p-abayes
-              - --p-no-abayes
-            argument: ""
-            description: Single branch test method.
+              - --m-accession-ids-file
+            argument: METADATA...
+            description: List of accession ids for sequences in the NCBI Protein database.
           - names:
-              - --p-lbp
-            argument: INTEGER
-            description: Single branch test method.
+              - --p-ranks
+            argument: TEXT...
+            description: List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy database.
           - names:
-              - --p-bnni
-              - --p-no-bnni
+              - --p-rank-propagation
+              - --p-no-rank-propagation
             argument: ""
-            description: Optimize UFBoot trees by NNI on bootstrap alignment.
+            description: Propagate known ranks to missing ranks if true
           - names:
-              - --p-safe
-              - --p-no-safe
-            argument: ""
-            description: Safe likelihood kernel to avoid numerical underflow.
+              - --p-n-jobs
+            argument: INTEGER
+            description: 'Number of concurrent download connections. More is faster until you run out of bandwidth. [default: 1]'
           - names:
-              - --o-tree
-            argument: ARTIFACT
-            description: The resulting phylogenetic tree.
+              - --o-sequences
+            argument: ARTIFACT FeatureData[ProteinSequence]
+            description: Sequences from the NCBI Protein database [required]
+          - names:
+              - --o-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomies from the NCBI Taxonomy database [required]
           - names:
               - --output-dir
             argument: PATH
@@ -8206,18 +13067,52 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: midpoint-root
-        description: Midpoint root an unrooted phylogenetic tree.
-        usage: qiime phylogeny midpoint-root [OPTIONS]
+      - name: get-ncbi-genomes
+        description: Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.
+        usage: qiime rescript get-ncbi-genomes [OPTIONS]
         options:
           - names:
-              - --i-tree
-            argument: ARTIFACT Phylogeny[Unrooted]
-            description: The phylogenetic tree to be rooted. [required]
+              - --p-taxon
+            argument: TEXT
+            description: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank. [required]
+          - names:
+              - --p-assembly-source
+            argument: TEXT Choices('refseq', 'genbank')
+            description: Fetch only RefSeq or GenBank genome assemblies.
+          - names:
+              - --p-assembly-levels
+            argument: TEXT... Choices('complete_genome', 'chromosome', 'scaffold', 'contig')
+            description: Fetch only genome assemblies that are one of the specified assembly levels.
+          - names:
+              - --p-only-reference
+              - --p-no-only-reference
+            argument: ""
+            description: 'Fetch only reference and representative genome assemblies. [default: True]'
+          - names:
+              - --p-tax-exact-match
+              - --p-no-tax-exact-match
+            argument: ""
+            description: 'If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too. [default: False]'
+          - names:
+              - --p-page-size
+            argument: INTEGER Range(20, 1000, inclusive_end=True)
+            description: 'The maximum number of genome assemblies to return per request. If number of genomes to fetch is higher than this number, requests will be repeated until all assemblies are fetched. [default: 20]'
+          - names:
+              - --o-genome-assemblies
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Nucleotide sequences of requested genomes. [required]
+          - names:
+              - --o-loci
+            argument: ARTIFACT
+            description: Loci features of requested genomes.
+          - names:
+              - --o-proteins
+            argument: ARTIFACT GenomeData[Proteins]
+            description: Protein sequences originating from requested genomes. [required]
           - names:
-              - --o-rooted-tree
-            argument: ARTIFACT
-            description: Phylogeny[Rooted] The rooted phylogenetic tree. [required]
+              - --o-taxonomies
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: Taxonomies of requested genomes. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -8239,34 +13134,33 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: raxml
-        description: Construct a phylogenetic tree with RAxML.
-        usage: qiime phylogeny raxml [OPTIONS]
+      - name: get-silva-data
+        description: Download, parse, and import SILVA database.
+        usage: qiime rescript get-silva-data [OPTIONS]
         options:
           - names:
-              - --i-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: Aligned sequences to be used for phylogenetic reconstruction. [required]
-          - names:
-              - --p-seed
-            argument: INTEGER
-            description: Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen.
+              - --p-include-species-labels
+              - --p-no-include-species-labels
+            argument: ""
+            description: 'Include species rank labels in taxonomy output. Note: species-labels may not be reliable in all cases. [default: False]'
           - names:
-              - --p-n-searches
-            argument: INTEGER
-            description: The number of independent maximum likelihood
+              - --p-rank-propagation
+              - --p-no-rank-propagation
+            argument: ""
+            description: 'If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for ''f__Pasteurellaceae; g__''then the ''f__'' rank will be propagated to become: ''f__Pasteurellaceae; g__Pasteurellaceae''.'
           - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML. [default: 1]'
+              - --p-download-sequences
+              - --p-no-download-sequences
+            argument: ""
+            description: 'Toggle whether or not to download and import the SILVA reference sequences associated with the release. Skipping the sequences is useful if you only want to download and parse the taxonomy, e.g., a local copy of the sequences already exists or for testing purposes. NOTE: if this option is used, a `silva-sequences` output is still created, but contains no data. [default: True]'
           - names:
-              - --p-raxml-version
-            argument: TEXT Choices('Standard', 'SSE3', 'AVX2')
-            description: Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version.
+              - --o-silva-sequences
+            argument: ARTIFACT FeatureData[RNASequence]
+            description: SILVA reference sequences. [required]
           - names:
-              - --o-tree
-            argument: ARTIFACT
-            description: The resulting phylogenetic tree.
+              - --o-silva-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: SILVA reference taxonomy. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -8276,6 +13170,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -8288,38 +13202,35 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: raxml-rapid-bootstrap
-        description: Construct a phylogenetic tree with bootstrap
-        usage: qiime phylogeny raxml-rapid-bootstrap [OPTIONS]
+      - name: get-unite-data
+        description: Download and import UNITE reference data.
+        usage: qiime rescript get-unite-data [OPTIONS]
         options:
           - names:
-              - --i-alignment
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: Aligned sequences to be used for phylogenetic reconstruction. [required]
+              - --p-version
+            argument: TEXT Choices('10.0', '9.0', '8.3', '8.2')
+            description: 'UNITE version to download. [default: ''10.0'']'
           - names:
-              - --p-seed
-            argument: INTEGER
-            description: Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen.
+              - --p-taxon-group
+            argument: TEXT Choices('fungi', 'eukaryotes')
+            description: 'Download a database with only ''fungi'' or including all ''eukaryotes''. [default: ''eukaryotes'']'
           - names:
-              - --p-rapid-bootstrap-seed
-            argument: INTEGER
-            description: Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen.
+              - --p-cluster-id
+            argument: TEXT Choices('99', '97', 'dynamic')
+            description: 'Percent similarity at which sequences in the of database were clustered. [default: ''99'']'
           - names:
-              - --p-bootstrap-replicates
+              - --p-singletons
+              - --p-no-singletons
             argument: ""
-            description: INTEGER
-          - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML. [default: 1]'
+            description: Include singleton clusters in the database.
           - names:
-              - --p-raxml-version
-            argument: TEXT Choices('Standard', 'SSE3', 'AVX2')
-            description: Select a specific CPU optimization of RAxML to use. The SSE3 versions will run approximately 40% faster than the standard version. The AVX2 version will run 10-30% faster than the SSE3 version.
+              - --o-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: UNITE reference taxonomy. [required]
           - names:
-              - --o-tree
-            argument: ARTIFACT
-            description: The resulting phylogenetic tree.
+              - --o-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: UNITE reference sequences. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -8341,26 +13252,34 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: robinson-foulds
-        description: Calculate Robinson-Foulds distance between
-        usage: qiime phylogeny robinson-foulds [OPTIONS]
+      - name: merge-taxa
+        description: Compare taxonomies and select the longest, highest scoring, or find the least common ancestor.
+        usage: qiime rescript merge-taxa [OPTIONS]
         options:
           - names:
-              - --i-trees
-            argument: ARTIFACTS... List[Phylogeny[Rooted | Unrooted]]
-            description: Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric. [required]
+              - --i-data
+            argument: ARTIFACTS... List[FeatureData[Taxonomy]]
+            description: Two or more feature taxonomies to be merged.
           - names:
-              - --p-labels
-            argument: TEXT...
-            description: Labels to use for the tree names in the distance
+              - --p-mode
+            argument: TEXT Choices('len', 'lca', 'score', 'super', 'majority')
+            description: 'How to merge feature taxonomies: "len" will select the taxonomy with the most elements (e.g., species level will beat genus level); "lca" will find the least common ancestor and report this consensus taxonomy; "score" will select the taxonomy with the highest score (e.g., confidence or consensus score). Note that "score" assumes that this score is always contained as the second column in a feature taxonomy dataframe. "majority" finds the LCA consensus while giving preference to majority labels. "super" finds the LCA consensus while giving preference to majority labels and collapsing substrings into superstrings. For example, when a more specific taxonomy does not contradict a less specific taxonomy, the more specific is chosen. That is, "g__Faecalibacterium; s__prausnitzii", will be preferred over "g__Faecalibacterium; s__" [default: ''len'']'
           - names:
-              - --p-missing-tips
-            argument: TEXT Choices('error', 'intersect-all')
-            description: 'How to handle tips that are not shared between trees. "error" will raise an error if the set of tips is not identical between all input trees. "intersect-all" will remove tips that are not shared between all trees before computing distances beteen trees. [default: ''error'']'
+              - --p-rank-handle-regex
+            argument: TEXT
+            description: 'Regular expression indicating which taxonomic rank a label belongs to; this handle is stripped from the label prior to operating on the taxonomy. The net effect is that ambiguous or empty levels can be removed prior to comparison, enabling selection of taxonomies with more complete taxonomic information. For example, "^[dkpcofgs]__" will recognize greengenes or silva rank handles. Note that rank_handles are removed but not replaced; use the new_rank_handle parameter to replace the rank handles. [default: ''^[dkpcofgs]__'']'
           - names:
-              - --o-distance-matrix
-            argument: ARTIFACT
-            description: DistanceMatrix The distances between trees as a symmetric matrix.
+              - --p-new-rank-handles
+            argument: VALUES...
+            description: Specifies the set of rank handles to prepend to taxonomic labels at each rank.
+          - names:
+              - --p-unclassified-label
+            argument: TEXT
+            description: Specifies what label should be used for taxonomies that could not be resolved (when LCA modes are used).
+          - names:
+              - --o-merged-data
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -8382,96 +13301,68 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: quality-control
-    description: Plugin for quality control of feature and sequence data.
-    usage: qiime quality-control [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: bowtie2-build
-        description: Build bowtie2 index from reference sequences.
-        usage: qiime quality-control bowtie2-build [OPTIONS]
+      - name: orient-seqs
+        description: Orient input sequences by comparison against reference.
+        usage: qiime rescript orient-seqs [OPTIONS]
         options:
           - names:
               - --i-sequences
             argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequences used to build bowtie2 index.
-          - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'Number of threads to launch.   [default: 1]'
+            description: Sequences to be oriented. [required]
           - names:
-              - --o-database
-            argument: ARTIFACT
-            description: Bowtie2 index.
+              - --i-reference-sequences
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Reference sequences to orient against. If no reference is provided, all the sequences will be reverse complemented and all parameters will be ignored. [optional]
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-threads
+            argument: INTEGER
+            description: Number of computation threads to use (1 to 256).
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --p-dbmask
+            argument: TEXT Choices('none', 'dust', 'soft')
+            description: Mask regions in the target database sequences using the dust method, or do not mask (none). When using soft masking, search commands become case sensitive.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-relabel
+            argument: TEXT
+            description: Relabel sequences using the prefix string and a ticker (1, 2, 3, etc.) to construct the new headers. Use --sizeout to conserve the abundance annotations.
           - names:
-              - --citations
+              - --p-relabel-keep
+              - --p-no-relabel-keep
             argument: ""
-            description: Show citations and exit.
+            description: When relabeling, keep the original identifier in the header after a space. [optional]
           - names:
-              - --help
+              - --p-relabel-md5
+              - --p-no-relabel-md5
             argument: ""
-            description: Show this message and exit.
-      - name: decontam-identify
-        description: Identify contaminants
-        usage: qiime quality-control decontam-identify [OPTIONS]
-        options:
-          - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Feature table which contaminate sequences will be identified from [required]
+            description: When relabeling, use the MD5 digest of the sequence as the new identifier. Use --sizeout to conserve the abundance annotations. [optional]
           - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter [required]
+              - --p-relabel-self
+              - --p-no-relabel-self
+            argument: ""
+            description: Relabel sequences using the sequence itself as a label. [optional]
           - names:
-              - --p-method
-            argument: TEXT Choices('combined', 'frequency', 'prevalence')
-            description: 'Select how to which method to id contaminants with; Prevalence: Utilizes control ASVs/OTUs to identify contaminants, Frequency: Utilizes sample concentration information to identify contaminants, Combined: Utilizes both Prevalence and Frequency methods when identifying contaminants [default: ''prevalence'']'
+              - --p-relabel-sha1
+              - --p-no-relabel-sha1
+            argument: ""
+            description: When relabeling, use the SHA1 digest of the sequence as the new identifier. The probability of a collision is smaller than the MD5 algorithm.
           - names:
-              - --p-freq-concentration-column
-            argument: TEXT
-            description: Input column name that has concentration information for the samples [optional]
+              - --p-sizein
+              - --p-no-sizein
+            argument: ""
+            description: In de novo mode, abundance annotations (pattern `[>;]size=integer[;]`) present in sequence headers are taken into account. [optional]
           - names:
-              - --p-prev-control-column
-            argument: TEXT
-            description: Input column name containing experimental or control sample metadata [optional]
+              - --p-sizeout
+              - --p-no-sizeout
+            argument: ""
+            description: Add abundance annotations to the output FASTA files. [optional]
           - names:
-              - --p-prev-control-indicator
-            argument: TEXT
-            description: indicate the control sample identifier (e.g. "control" or "blank") [optional]
+              - --o-oriented-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Query sequences in same orientation as top matching reference sequence. [required]
           - names:
-              - --o-decontam-scores
-            argument: ARTIFACT FeatureData[DecontamScore]
-            description: The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence [required]
+              - --o-unmatched-seqs
+            argument: ARTIFACT FeatureData[Sequence]
+            description: Query sequences that fail to match at least one reference sequence in either + or - orientation. This will be empty if no refrence is provided.
           - names:
               - --output-dir
             argument: PATH
@@ -8493,72 +13384,36 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: decontam-identify-batches
-        description: Identify contaminants in Batch Mode
-        usage: qiime quality-control decontam-identify-batches [OPTIONS]
+      - name: parse-silva-taxonomy
+        description: Generates a SILVA fixed-rank taxonomy.
+        usage: qiime rescript parse-silva-taxonomy [OPTIONS]
         options:
           - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Feature table which contaminate sequences will be identified from [required]
-          - names:
-              - --i-rep-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Representative Sequences table which contaminate seqeunces will be removed from [optional]
-          - names:
-              - --m-metadata-file
-            argument: METADATA...
-            description: metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter [required]
+              - --i-taxonomy-map
+            argument: ARTIFACT FeatureData[SILVATaxidMap]
+            description: 'SILVA taxonomy map. This file contains a mapping of the sequence accessions to the numeric taxonomy identifiers and species label information. The SILVA release filename is typically in the form of: ''taxmap_slv_ssu_ref_X.txt'', or ''taxmap_slv_ssu_ref_nr_X.txt'' where ''X'' is the SILVA version number. [required]'
           - names:
-              - --p-split-column
-            argument: TEXT
-            description: 'input metadata columns that you wish to subset the ASV table byNote: Column names must be in quotes and delimited by a space [required]'
+              - --i-taxonomy-ranks
+            argument: ARTIFACT FeatureData[SILVATaxonomy]
+            description: 'SILVA taxonomy file. This file contains the taxonomic rank information for each numeric taxonomy identifier and the taxonomy. The SILVA filename typically takes the form of: ''tax_slv_ssu_X.txt'', where ''X'' is the SILVA version number. [required]'
           - names:
-              - --p-method
-            argument: TEXT Choices('combined', 'frequency', 'prevalence')
-            description: 'Select how to which method to id contaminants with; Prevalence: Utilizes control ASVs/OTUs to identify contaminants, Frequency: Utilizes sample concentration information to identify contaminants, Combined: Utilizes both Prevalence and Frequency methods when identifying contaminants [required]'
+              - --i-taxonomy-tree
+            argument: ARTIFACT
+            description: Phylogeny[Rooted] SILVA hierarchical taxonomy tree. The SILVA release
           - names:
-              - --p-filter-empty-features
-              - --p-no-filter-empty-features
+              - --p-rank-propagation
+              - --p-no-rank-propagation
             argument: ""
-            description: If true, features which are not present in a split feature table are dropped. [optional]
-          - names:
-              - --p-freq-concentration-column
-            argument: TEXT
-            description: Input column name that has concentration information for the samples [optional]
-          - names:
-              - --p-prev-control-column
-            argument: TEXT
-            description: Input column name containing experimental or control sample metadata [optional]
-          - names:
-              - --p-prev-control-indicator
-            argument: TEXT
-            description: indicate the control sample identifier (e.g. "control" or "blank") [optional]
-          - names:
-              - --p-threshold
-            argument: NUMBER
-            description: 'Select threshold cutoff for decontam algorithm scores [default: 0.1]'
+            description: 'If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for ''f__Pasteurellaceae; g__''then the ''f__'' rank will be propagated to become: ''f__Pasteurellaceae; g__Pasteurellaceae''.'
           - names:
-              - --p-weighted
-              - --p-no-weighted
+              - --p-include-species-labels
+              - --p-no-include-species-labels
             argument: ""
-            description: 'weight the decontam scores by their associated read number [default: True]'
-          - names:
-              - --p-bin-size
-            argument: NUMBER
-            description: 'Select bin size for the histogram [default: 0.02]'
-          - names:
-              - --o-batch-subset-tables
-            argument: ARTIFACTS... Collection[FeatureTable[Frequency]]
-            description: Directory where feature tables split based on metadata and parameter split-column values should be written. [required]
-          - names:
-              - --o-decontam-scores
-            argument: ARTIFACTS... Collection[FeatureData[DecontamScore]]
-            description: The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence [required]
+            description: 'Include species rank labels in taxonomy output. Note: species-labels may not be reliable in all cases. [default: False]'
           - names:
-              - --o-score-histograms
-            argument: VISUALIZATION
-            description: The vizulaizer histograms for all decontam score objects generated from the pipeline [required]
+              - --o-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: The resulting fixed-rank formatted SILVA taxonomy.
           - names:
               - --output-dir
             argument: PATH
@@ -8568,26 +13423,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -8600,34 +13435,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: decontam-remove
-        description: Remove contaminants
-        usage: qiime quality-control decontam-remove [OPTIONS]
+      - name: reverse-transcribe
+        description: Reverse transcribe RNA to DNA sequences.
+        usage: qiime rescript reverse-transcribe [OPTIONS]
         options:
           - names:
-              - --i-decontam-scores
-            argument: ARTIFACT FeatureData[DecontamScore]
-            description: Pre-feature decontam scores. [required]
-          - names:
-              - --i-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Feature table from which contaminants will be removed. [required]
-          - names:
-              - --i-rep-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Feature representative sequences from which contaminants will be removed. [required]
-          - names:
-              - --p-threshold
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: Decontam score threshold. Features with a score less than or equal to this threshold will be removed.
-          - names:
-              - --o-filtered-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Feature table with contaminants removed. [required]
+              - --i-rna-sequences
+            argument: ARTIFACT FeatureData
+            description: RNA Sequences to reverse transcribe to DNA. [required]
           - names:
-              - --o-filtered-rep-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Feature representative sequences with contaminants removed. [required]
+              - --o-dna-sequences
+            argument: ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]
+            description: Reverse-transcribed DNA sequences. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -8649,39 +13468,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: decontam-score-viz
-        description: Generate a histogram representation of the scores
-        usage: qiime quality-control decontam-score-viz [OPTIONS]
+      - name: subsample-fasta
+        description: Subsample an indicated number of sequences from a FASTA file.
+        usage: qiime rescript subsample-fasta [OPTIONS]
         options:
           - names:
-              - --i-decontam-scores
-            argument: ARTIFACTS... Collection[FeatureData[DecontamScore]]
-            description: Output from decontam identify to be visualized
-          - names:
-              - --i-table
-            argument: ARTIFACTS... Collection[FeatureTable[Frequency]]
-            description: Raw OTU/ASV table that was used as input to decontam-identify [required]
-          - names:
-              - --i-rep-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Representative Sequences table which contaminate sequences will be removed from [optional]
-          - names:
-              - --p-threshold
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: 'Select threshold cutoff for decontam algorithm scores [default: 0.1]'
-          - names:
-              - --p-weighted
-              - --p-no-weighted
-            argument: ""
-            description: 'weight the decontam scores by their associated read number [default: True]'
-          - names:
-              - --p-bin-size
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: 'Select bin size for the histogram [default: 0.02]'
+              - --i-sequences
+            argument: ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]
+            description: Sequences to subsample from. [required]
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-sample-sequences
+            argument: ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]
+            description: Sample of original sequences. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -8703,71 +13501,34 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: evaluate-composition
-        description: Evaluate expected vs. observed taxonomic composition of samples
-        usage: qiime quality-control evaluate-composition [OPTIONS]
+      - name: trim-alignment
+        description: Trim alignment based on provided primers or specific positions.
+        usage: qiime rescript trim-alignment [OPTIONS]
         options:
           - names:
-              - --i-expected-features
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Expected feature compositions [required]
-          - names:
-              - --i-observed-features
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Observed feature compositions [required]
-          - names:
-              - --p-depth
-            argument: INTEGER
-            description: 'Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [default: 7]'
-          - names:
-              - --p-plot-tar
-              - --p-no-plot-tar
-            argument: ""
-            description: 'Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true positive features divided by the total number of observed features (TAR = true positives / (true positives + false positives)). [default: True]'
-          - names:
-              - --p-plot-tdr
-              - --p-no-plot-tdr
-            argument: ""
-            description: 'Plot taxon detection rate (TDR) on score plot. TDR is the number of true positive features divided by the total number of expected features (TDR = true positives / (true positives + false negatives)). [default: True]'
-          - names:
-              - --p-plot-r-value
-              - --p-no-plot-r-value
-            argument: ""
-            description: 'Plot expected vs. observed linear regression r value on score plot. [default: False]'
-          - names:
-              - --p-plot-r-squared
-              - --p-no-plot-r-squared
-            argument: ""
-            description: 'Plot expected vs. observed linear regression r-squared value on score plot. [default: True]'
-          - names:
-              - --p-plot-bray-curtis
-              - --p-no-plot-bray-curtis
-            argument: ""
-            description: 'Plot expected vs. observed Bray-Curtis dissimilarity scores on score plot. [default: False]'
-          - names:
-              - --p-plot-jaccard
-              - --p-no-plot-jaccard
-            argument: ""
-            description: 'Plot expected vs. observed Jaccard distances scores on score plot. [default: False]'
+              - --i-aligned-sequences
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: Aligned DNA sequences. [required]
           - names:
-              - --p-plot-observed-features
-              - --p-no-plot-observed-features
-            argument: ""
-            description: Plot observed features count on score plot.
+              - --p-primer-fwd
+            argument: TEXT
+            description: Forward primer used to find the start position for alignment trimming. [optional]
           - names:
-              - --p-plot-observed-features-ratio
-              - --p-no-plot-observed-features-ratio
-            argument: ""
-            description: 'Plot ratio of observed:expected features on score plot. [default: True]'
+              - --p-primer-rev
+            argument: TEXT
+            description: Reverse primer used to find the end position for alignment trimming. [optional]
           - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs. [optional]
+              - --p-position-start
+            argument: INTEGER
+            description: Position within the alignment where the trimming will begin.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --p-position-end
+            argument: INTEGER
+            description: Position within the alignment where the trimming will end.
+          - names:
+              - --o-trimmed-sequences
+            argument: ARTIFACT FeatureData[AlignedSequence]
+            description: Trimmed sequence alignment. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -8778,47 +13539,25 @@ subcommands:
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
-          - names:
-              - --citations
-            argument: ""
-            description: Show citations and exit.
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
           - names:
-              - --help
+              - --no-recycle
             argument: ""
-            description: Show this message and exit.
-      - name: evaluate-seqs
-        description: Compare query (observed) vs. reference (expected) sequences.
-        usage: qiime quality-control evaluate-seqs [OPTIONS]
-        options:
-          - names:
-              - --i-query-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences to test for exclusion [required]
-          - names:
-              - --i-reference-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequences to align against feature sequences
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
           - names:
-              - --p-show-alignments
-              - --p-no-show-alignments
+              - --parallel
             argument: ""
-            description: 'Option to plot pairwise alignments of query sequences and their top hits. [default: False]'
-          - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+            description: Execute your action in parallel. This flag will use your default parallel config.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -8831,44 +13570,122 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: evaluate-taxonomy
-        description: Evaluate expected vs. observed taxonomic assignments
-        usage: qiime quality-control evaluate-taxonomy [OPTIONS]
+  - name: sample-classifier
+    description: Plugin for machine learning prediction of sample
+    usage: qiime sample-classifier [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: classify-samples
+        description: Train and test a cross-validated supervised
+        usage: qiime sample-classifier classify-samples [OPTIONS]
         options:
           - names:
-              - --i-expected-taxa
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Expected taxonomic assignments [required]
+              - --i-table
+            argument: ARTIFACT
+            description: Feature table containing all features that should be used for target prediction. [required]
           - names:
-              - --i-observed-taxa
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Observed taxonomic assignments [required]
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Categorical metadata column to use as prediction target. [required]
           - names:
-              - --i-feature-table
-            argument: ARTIFACT FeatureTable[RelativeFrequency]
-            description: Optional feature table containing relative frequency of each feature, used to weight accuracy scores by frequency. Must contain all features found in expected and/or observed taxa. Features found in the table but not the expected/observed taxa will be dropped prior to analysis. [optional]
+              - --p-test-size
+            argument: PROPORTION
+            description: Fraction of input samples to exclude from training set and use for classifier testing.
           - names:
-              - --p-depth
+              - --p-step
+            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
+            description: If optimize-feature-selection is True, step is the percentage of features to remove at each iteration.
+          - names:
+              - --p-cv
             argument: INTEGER
-            description: Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [required]
+            description: Number of k-fold cross-validations to perform.
           - names:
-              - --p-require-exp-ids
-              - --p-no-require-exp-ids
+              - --p-random-state
+            argument: INTEGER
+            description: Seed used by random number generator. [optional]
+          - names:
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'Number of jobs to run in parallel. [default: 1]'
+          - names:
+              - --p-n-estimators
+            argument: INTEGER
+            description: Number of trees to grow for estimation.
+          - names:
+              - --p-estimator
+            argument: '{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}'
+            description: Estimator method to use for sample prediction.
+          - names:
+              - --p-optimize-feature-selection
+              - --p-no-optimize-feature-selection
             argument: ""
-            description: Require that all features found in observed taxa must be found in expected taxa or raise error.
+            description: Automatically optimize input feature selection using recursive feature elimination.
           - names:
-              - --p-require-obs-ids
-              - --p-no-require-obs-ids
+              - --p-parameter-tuning
+              - --p-no-parameter-tuning
             argument: ""
-            description: Require that all features found in expected taxa must be found in observed taxa or raise error.
+            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
           - names:
-              - --p-sample-id
+              - --p-palette
             argument: TEXT
-            description: Optional sample ID to use for extracting frequency data from feature table, and for labeling accuracy results. If no sample-id is provided, feature frequencies are derived from the sum of all samples present in the feature table. [optional]
+            description: The color palette to use for plotting.
           - names:
-              - --o-visualization
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+          - names:
+              - --o-sample-estimator
+            argument: ARTIFACT SampleEstimator[Classifier]
+            description: Trained sample estimator. [required]
+          - names:
+              - --o-feature-importance
+            argument: ARTIFACT FeatureData[Importance]
+            description: Importance of each input feature to model accuracy.
+          - names:
+              - --o-predictions
+            argument: ARTIFACT SampleData[ClassifierPredictions]
+            description: Predicted target values for each input sample.
+          - names:
+              - --o-model-summary
             argument: VISUALIZATION
-            description: '[required]'
+            description: Summarized parameter and (if enabled) feature selection information for the trained estimator.
+          - names:
+              - --o-accuracy-results
+            argument: VISUALIZATION
+            description: Accuracy results visualization. [required]
+          - names:
+              - --o-probabilities
+            argument: ARTIFACT SampleData[Probabilities]
+            description: Predicted class probabilities for each input sample. [required]
+          - names:
+              - --o-heatmap
+            argument: VISUALIZATION
+            description: A heatmap of the top 50 most important features from the table. [required]
+          - names:
+              - --o-training-targets
+            argument: ARTIFACT SampleData[TrueTargets]
+            description: Series containing true target values of train samples [required]
+          - names:
+              - --o-test-targets
+            argument: ARTIFACT SampleData[TrueTargets]
+            description: Series containing true target values of test samples [required]
           - names:
               - --output-dir
             argument: PATH
@@ -8878,6 +13695,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -8890,42 +13727,47 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: exclude-seqs
-        description: Exclude sequences by alignment
-        usage: qiime quality-control exclude-seqs [OPTIONS]
+      - name: classify-samples-from-dist
+        description: Run k-nearest-neighbors on a labeled distance
+        usage: qiime sample-classifier classify-samples-from-dist [OPTIONS]
         options:
           - names:
-              - --i-query-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences to test for exclusion [required]
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: DistanceMatrix a distance matrix [required]
           - names:
-              - --i-reference-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequences to align against feature sequences [required]
+              - --p-k
+            argument: INTEGER
+            description: 'Number of nearest neighbors [default: 1]'
           - names:
-              - --p-perc-identity
-            argument: PROPORTION Range(0.0, 1.0, inclusive_end=True)
-            description: 'Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0] [default: 0.97]'
+              - --p-cv
+            argument: INTEGER
+            description: Number of k-fold cross-validations to perform.
           - names:
-              - --p-evalue
-            argument: NUMBER
-            description: BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default. [optional]
+              - --p-n-jobs
+            argument: NTHREADS
+            description: Number of jobs to run in parallel.
           - names:
-              - --p-perc-query-aligned
-            argument: NUMBER
-            description: Percent of query sequence that must align to reference in order to be accepted as a hit.
+              - --p-palette
+            argument: TEXT
+            description: The color palette to use for plotting.
           - names:
-              - --p-threads
-            argument: NTHREADS
-            description: 'Number of threads to use. Only applies to vsearch method. [default: 1]'
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Categorical metadata column to use as prediction target. [required]
           - names:
-              - --o-sequence-hits
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Subset of feature sequences that align to reference sequences [required]
+              - --p-random-state
+            argument: INTEGER
+            description: Seed used by random number generator. [optional]
+          - names:
+              - --o-predictions
+            argument: ARTIFACT SampleData[ClassifierPredictions]
+            description: leave one out predictions for each sample [required]
           - names:
-              - --o-sequence-misses
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Subset of feature sequences that do not align to reference sequences [required]
+              - --o-accuracy-results
+            argument: VISUALIZATION
+            description: Accuracy results visualization. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -8936,55 +13778,25 @@ subcommands:
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
-          - names:
-              - --citations
-            argument: ""
-            description: Show citations and exit.
-          - names:
-              - --help
-            argument: ""
-            description: Show this message and exit.
-      - name: filter-reads
-        description: Filter demultiplexed sequences by alignment to reference database.
-        usage: qiime quality-control filter-reads [OPTIONS]
-        options:
-          - names:
-              - --i-database
-            argument: ARTIFACT
-            description: Bowtie2 indexed database.
-          - names:
-              - --p-n-threads
-            argument: NTHREADS
-            description: 'Number of alignment threads to launch. [default: 1]'
-          - names:
-              - --p-mode
-            argument: TEXT Choices('local', 'global')
-            description: 'Bowtie2 alignment settings. See bowtie2 manual for more details. [default: ''local'']'
-          - names:
-              - --p-ref-gap-open-penalty
-            argument: ""
-            description: INTEGER
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
           - names:
-              - --p-ref-gap-ext-penalty
+              - --no-recycle
             argument: ""
-            description: INTEGER
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
           - names:
-              - --p-exclude-seqs
-              - --p-no-exclude-seqs
+              - --parallel
             argument: ""
-            description: 'Exclude sequences that align to reference. Set this option to False to exclude sequences that do not align to the reference database. [default: True]'
+            description: Execute your action in parallel. This flag will use your default parallel config.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -8997,71 +13809,60 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: quality-filter
-    description: Plugin for PHRED-based filtering and trimming.
-    usage: qiime quality-filter [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-  - name: rescript
-    description: Pipeline for reference sequence annotation and curation.
-    usage: qiime rescript [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: cull-seqs
-        description: Removes sequences that contain at least the specified number of degenerate bases and/or homopolymers of a given length.
-        usage: qiime rescript cull-seqs [OPTIONS]
+      - name: classify-samples-ncv
+        description: Nested cross-validated supervised learning
+        usage: qiime sample-classifier classify-samples-ncv [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[Sequence | RNASequence]
-            description: DNA or RNA Sequences to be screened for removal based on degenerate base and homopolymer screening criteria. [required]
+            - --i-table
+            argument: ARTIFACT
+            description: Feature table containing all features that should be used for target prediction. [required]
           - names:
-              - --p-num-degenerates
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Categorical metadata column to use as prediction target. [required]
+          - names:
+              - --p-cv
             argument: INTEGER
-            description: Sequences with N, or more, degenerate bases will be removed.
+            description: Number of k-fold cross-validations to perform.
           - names:
-              - --p-homopolymer-length
+              - --p-random-state
             argument: INTEGER
-            description: Sequences containing a homopolymer sequence of length N, or greater, will be removed.
+            description: Seed used by random number generator. [optional]
           - names:
               - --p-n-jobs
+            argument: NTHREADS
+            description: 'Number of jobs to run in parallel. [default: 1]'
+          - names:
+              - --p-n-estimators
             argument: INTEGER
-            description: Number of concurrent processes to use while processing sequences.
+            description: Number of trees to grow for estimation.
           - names:
-              - --o-clean-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The resulting DNA sequences that pass degenerate base and homopolymer screening criteria. [required]
+              - --p-estimator
+            argument: '{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}'
+            description: Estimator method to use for sample prediction.
+          - names:
+              - --p-parameter-tuning
+              - --p-no-parameter-tuning
+            argument: ""
+            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
+          - names:
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+          - names:
+              - --o-predictions
+            argument: ARTIFACT SampleData[ClassifierPredictions]
+            description: Predicted target values for each input sample.
+          - names:
+              - --o-feature-importance
+            argument: ARTIFACT FeatureData[Importance]
+            description: Importance of each input feature to model accuracy.
+          - names:
+              - --o-probabilities
+            argument: ARTIFACT SampleData[Probabilities]
+            description: Predicted class probabilities for each input sample.
           - names:
               - --output-dir
             argument: PATH
@@ -9083,22 +13884,31 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: degap-seqs
-        description: Remove gaps from DNA sequence alignments.
-        usage: qiime rescript degap-seqs [OPTIONS]
+      - name: confusion-matrix
+        description: Make a confusion matrix from sample classifier
+        usage: qiime sample-classifier confusion-matrix [OPTIONS]
         options:
           - names:
-              - --i-aligned-sequences
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: Aligned DNA Sequences to be degapped. [required]
+              - --i-predictions
+            argument: ARTIFACT SampleData[ClassifierPredictions]
+            description: Predicted values to plot on x axis. Should be predictions of categorical data produced by a sample classifier. [required]
           - names:
-              - --p-min-length
-            argument: INTEGER
-            description: 'Minimum length of sequence to be returned after degapping. [default: 1]'
+              - --i-probabilities
+            argument: ARTIFACT SampleData[Probabilities]
+            description: Predicted class probabilities for each input sample.
           - names:
-              - --o-degapped-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: The resulting unaligned (degapped) DNA sequences.
+              - --m-truth-file
+              - --m-truth-column
+            argument: METADATA
+            description: Metadata column (true values) to plot on y axis.
+          - names:
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+          - names:
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -9120,43 +13930,65 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: dereplicate
-        description: Dereplicate features with matching sequences and taxonomies.
-        usage: qiime rescript dereplicate [OPTIONS]
+      - name: fit-classifier
+        description: Fit a supervised learning classifier.
+        usage: qiime sample-classifier fit-classifier [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences to be dereplicated [required]
+            - --i-table
+            argument: ARTIFACT
+            description: Feature table containing all features that should be used for target prediction. [required]
           - names:
-              - --i-taxa
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomic classifications of sequences to be dereplicated [required]
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Numeric metadata column to use as prediction target.
           - names:
-              - --p-mode
-            argument: TEXT Choices('uniq', 'lca', 'majority', 'super')
-            description: How to handle dereplication when sequences map to distinct taxonomies. "uniq" will retain all sequences with unique taxonomic affiliations. "lca" will find the least common ancestor among all taxa sharing a sequence. "majority" will find the most common taxonomic label associated with that sequence; note that in the event of a tie, "majority" will pick the winner arbitrarily. "super" finds the LCA consensus while giving preference to majority labels and collapsing substrings into superstrings. For example, when a more specific taxonomy does not contradict a less specific taxonomy, the more specific is chosen. That is, "g__Faecalibacterium; s__prausnitzii", will be preferred over "g__Faecalibacterium; s__"
+              - --p-step
+            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
+            description: If optimize-feature-selection is True, step is the percentage of features to remove at each iteration. [required]
           - names:
-              - --p-threads
+              - --p-cv
             argument: INTEGER
-            description: Number of computation threads to use (1 to 256).
+            description: Number of k-fold cross-validations to perform.
           - names:
-              - --p-rank-handles
-            argument: VALUES...
-            description: Specifies the set of rank handles used to backfill missing ranks in the resulting dereplicated taxonomy.
+              - --p-random-state
+            argument: INTEGER
+            description: Seed used by random number generator. [optional]
           - names:
-              - --p-derep-prefix
-              - --p-no-derep-prefix
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'Number of jobs to run in parallel. [default: 1]'
+          - names:
+              - --p-n-estimators
+            argument: INTEGER
+            description: Number of trees to grow for estimation.
+          - names:
+              - --p-estimator
+            argument: '{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}'
+            description: Estimator method to use for sample prediction.
+          - names:
+              - --p-optimize-feature-selection
+              - --p-no-optimize-feature-selection
             argument: ""
-            description: 'Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False]'
+            description: 'Automatically optimize input feature selection using recursive feature elimination. [default: False]'
+          - names:
+              - --p-parameter-tuning
+              - --p-no-parameter-tuning
+            argument: ""
+            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
+          - names:
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
           - names:
-              - --o-dereplicated-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: '[required]'
+              - --o-sample-estimator
+            argument: ARTIFACT SampleEstimator[Classifier]
+            description: Trained sample classifier. [required]
           - names:
-              - --o-dereplicated-taxa
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: '[required]'
+              - --o-feature-importance
+            argument: ARTIFACT FeatureData[Importance]
+            description: Importance of each input feature to model accuracy. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -9178,80 +14010,65 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: edit-taxonomy
-        description: Edit taxonomy strings with find and replace terms.
-        usage: qiime rescript edit-taxonomy [OPTIONS]
+      - name: fit-regressor
+        description: Fit a supervised learning regressor.
+        usage: qiime sample-classifier fit-regressor [OPTIONS]
         options:
           - names:
-              - --i-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomy strings data to be edited. [required]
-          - names:
-              - --m-replacement-map-file
-            argument: ""
-            description: METADATA
-          - names:
-              - --m-replacement-map-column
-            argument: COLUMN  MetadataColumn[Categorical]
-            description: A tab-delimitad metadata file in which the strings in the 'id' column are replaced by the 'replacement-strings' in the second column. All strings in the 'id' column must be unique! [optional]
+            - --i-table
+            argument: ARTIFACT
+            description: Feature table containing all features that should be used for target prediction. [required]
           - names:
-              - --p-search-strings
-            argument: TEXT...
-            description: Only used in conjuntion with 'replacement-strings'.
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Numeric metadata column to use as prediction target. [required]
           - names:
-              - --p-replacement-strings
-            argument: TEXT...
-            description: Only used in conjuntion with 'search-strings'.
+              - --p-step
+            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
+            description: If optimize-feature-selection is True, step is the percentage of features to remove at each iteration.
           - names:
-              - --p-use-regex
-              - --p-no-use-regex
-            argument: ""
-            description: Toggle regular expressions. By default, only litereal substring matching is performed.
+              - --p-cv
+            argument: INTEGER
+            description: Number of k-fold cross-validations to perform.
           - names:
-              - --o-edited-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomy in which the original strings are replaced by user-supplied strings. [required]
+              - --p-random-state
+            argument: INTEGER
+            description: Seed used by random number generator. [optional]
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'Number of jobs to run in parallel. [default: 1]'
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --p-n-estimators
+            argument: INTEGER
+            description: Number of trees to grow for estimation.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-estimator
+            argument: '{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor[DecisionTree], AdaBoostRegressor[ExtraTrees], ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}'
+            description: Estimator method to use for sample prediction.
           - names:
-              - --citations
+              - --p-optimize-feature-selection
+              - --p-no-optimize-feature-selection
             argument: ""
-            description: Show citations and exit.
+            description: 'Automatically optimize input feature selection using recursive feature elimination. [default: False]'
           - names:
-              - --help
+              - --p-parameter-tuning
+              - --p-no-parameter-tuning
             argument: ""
-            description: Show this message and exit.
-      - name: evaluate-classifications
-        description: Interactively evaluate taxonomic classification accuracy.
-        usage: qiime rescript evaluate-classifications [OPTIONS]
-        options:
-          - names:
-              - --i-expected-taxonomies
-            argument: ARTIFACTS... List[FeatureData[Taxonomy]]
-            description: True taxonomic labels for one more more sets of features. [required]
+            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
           - names:
-              - --i-observed-taxonomies
-            argument: ARTIFACTS... List[FeatureData[Taxonomy]]
-            description: Predicted classifications of same sets of features, input in same order as expected-taxonomies.
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: How to handle missing samples in metadata.
           - names:
-              - --p-labels
-            argument: TEXT...
-            description: List of labels to use for labeling evaluation
+              - --o-sample-estimator
+            argument: ARTIFACT SampleEstimator[Regressor]
+            description: 'Trained sample regressor. [required]'
           - names:
-              - --o-evaluation
-            argument: VISUALIZATION
-            description: Visualization of classification accuracy results.
+              - --o-feature-importance
+            argument: ARTIFACT FeatureData[Importance]
+            description: Importance of each input feature to model accuracy. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -9261,26 +14078,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -9293,50 +14090,74 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: evaluate-cross-validate
-        description: Evaluate DNA sequence reference database via cross-validated taxonomic classification.
-        usage: qiime rescript evaluate-cross-validate [OPTIONS]
+      - name: heatmap
+        description: Generate heatmap of important features.
+        usage: qiime sample-classifier heatmap [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequences to use for classifier training/testing. [required]
+            - --i-table
+            argument: ARTIFACT
+            description: Feature table containing all features that should be used for target prediction. [required]
           - names:
-              - --i-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Reference taxonomy to use for classifier training/testing. [required]
+              - --i-importance
+            argument: ARTIFACT FeatureData[Importance]
+            description: Feature importances. [required]
           - names:
-              - --p-k
-            argument: INTEGER
-            description: Number of stratified folds.
+              - --m-sample-metadata-file
+              - --m-sample-metadata-column
+            argument: METADATA
+            description: Sample metadata column to use for sample labeling or grouping. [optional]
           - names:
-              - --p-random-state
+              - --m-feature-metadata-file
+              - --m-feature-metadata-column
+            argument: METADATA
+            description: Feature metadata (e.g., taxonomy) to use for labeling features in the heatmap. [optional]
+          - names:
+              - --p-feature-count
             argument: INTEGER
-            description: Seed used by the random number generator.
+            description: Filter feature table to include top N most important features.
           - names:
-              - --p-reads-per-batch
-            argument: VALUE
-            description: Number of reads to process in each batch. If "auto", this parameter is autoscaled to min( number of query sequences / n-jobs, 20000).
+              - --p-importance-threshold
+            argument: NUMBER
+            description: Filter feature table to include top N most important features.
           - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]'
+              - --p-group-samples
+              - --p-no-group-samples
+            argument: ""
+            description: 'Group samples by sample metadata. [default: False]'
           - names:
-              - --p-confidence
-            argument: VALUE
-            description: Confidence threshold for limiting taxonomic depth.
+              - --p-normalize
+              - --p-no-normalize
+            argument: ""
+            description: Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table.
           - names:
-              - --o-expected-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Expected taxonomic label for each input sequence. Taxonomic labels may be truncated due to k-fold CV and stratification. [required]
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''ignore'']'
           - names:
-              - --o-observed-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Observed taxonomic label for each input sequence, predicted by cross-validation. [required]
+              - --p-metric
+            argument: TEXT
+            description: Metrics exposed by seaborn
           - names:
-              - --o-evaluation
+              - --p-method
+            argument: TEXT
+            description: Clustering methods exposed by seaborn
+          - names:
+              - --p-cluster
+            argument: TEXT Choices('both', 'features', 'none', 'samples')
+            description: 'Specify which axes to cluster. [default: ''features'']'
+          - names:
+              - --p-color-scheme
+            argument: TEXT
+            description: Color scheme for heatmap.
+          - names:
+              - --o-heatmap
             argument: VISUALIZATION
-            description: Visualization of cross-validated accuracy results. [required]
+            description: Heatmap of important features. [required]
+          - names:
+              - --o-filtered-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Filtered feature table containing data displayed in heatmap. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -9378,42 +14199,35 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: evaluate-fit-classifier
-        description: Evaluate and train naive Bayes classifier on reference sequences.
-        usage: qiime rescript evaluate-fit-classifier [OPTIONS]
+      - name: metatable
+        description: Convert (and merge) positive numeric metadata
+        usage: qiime sample-classifier metatable [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequences to use for classifier training/testing. [required]
-          - names:
-              - --i-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Reference taxonomy to use for classifier training/testing. [required]
-          - names:
-              - --p-reads-per-batch
-            argument: VALUE
-            description: Number of reads to process in each batch. If "auto", this parameter is autoscaled to min( number of query sequences / n-jobs, 20000).
-          - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'The maximum number of concurrent worker processes. If 0 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. [default: 1]'
+              - --i-table
+            argument: ARTIFACT
+            description: Feature table containing all features that should be used for target prediction.
           - names:
-              - --p-confidence
-            argument: VALUE
-            description: Confidence threshold for limiting taxonomic depth.
+              - --m-metadata-file
+            argument: METADATA...
+            description: Metadata file to convert to feature table. [required]
           - names:
-              - --o-classifier
-            argument: ARTIFACT
-            description: Trained naive Bayes taxonomic classifier. [required]
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''ignore'']'
           - names:
-              - --o-evaluation
-            argument: VISUALIZATION
-            description: Visualization of classification accuracy results. [required]
+              - --p-missing-values
+            argument: TEXT Choices('drop_samples', 'drop_features', 'error', 'fill')
+            description: How to handle missing values (nans) in metadata.
           - names:
-              - --o-observed-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Observed taxonomic label for each input sequence, predicted by the trained classifier. [required]
+              - --p-drop-all-unique
+              - --p-no-drop-all-unique
+            argument: ""
+            description: 'If True, columns that contain a unique value for every ID will be dropped. [default: False]'
+          - names:
+              - --o-converted-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Converted feature table [required]
           - names:
               - --output-dir
             argument: PATH
@@ -9455,34 +14269,26 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: evaluate-seqs
-        description: Compute summary statistics on sequence artifact(s).
-        usage: qiime rescript evaluate-seqs [OPTIONS]
+      - name: predict-classification
+        description: Use trained classifier to predict target values
+        usage: qiime sample-classifier predict-classification [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACTS... List[FeatureData[Sequence]]
-            description: One or more sets of sequences to evaluate. [required]
-          - names:
-              - --p-labels
-            argument: TEXT...
-            description: List of labels to use for labeling evaluation results in the resulting visualization.
-          - names:
-              - --p-kmer-lengths
-            argument: INTEGERS...
-            description: Sequence kmer lengths to optionally use for entropy calculation.
+              - --i-sample-estimator
+            argument: ARTIFACT SampleEstimator[Classifier]
+            description: Sample classifier trained with fit_classifier.
           - names:
-              - --p-subsample-kmers
-            argument: PROPORTION
-            description: Optionally subsample sequences prior to kmer entropy measurement.
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'Number of jobs to run in parallel.   [default: 1]'
           - names:
-              - --p-palette
-            argument: TEXT
-            description: Color palette to use for plotting evaluation results.
+              - --o-predictions
+            argument: ARTIFACT SampleData[ClassifierPredictions]
+            description: Predicted target values for each input sample.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-probabilities
+            argument: ARTIFACT SampleData[Probabilities]
+            description: Predicted class probabilities for each input sample.
           - names:
               - --output-dir
             argument: PATH
@@ -9504,26 +14310,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: evaluate-taxonomy
-        description: Compute summary statistics on taxonomy artifact(s).
-        usage: qiime rescript evaluate-taxonomy [OPTIONS]
+      - name: predict-regression
+        description: Use trained regressor to predict target values
+        usage: qiime sample-classifier predict-regression [OPTIONS]
         options:
           - names:
-              - --i-taxonomies
-            argument: ARTIFACTS... List[FeatureData[Taxonomy]]
-            description: One or more taxonomies to evaluate. [required]
-          - names:
-              - --p-labels
-            argument: TEXT...
-            description: List of labels to use for labeling evaluation results in the resulting visualization.
+              - --i-sample-estimator
+            argument: ARTIFACT SampleEstimator[Regressor]
+            description: Sample regressor trained with fit_regressor. [required]
           - names:
-              - --p-rank-handle-regex
-            argument: TEXT
-            description: Regular expression indicating which taxonomic rank a label belongs to; this handle is stripped from the label prior to operating on the taxonomy. The net effect is that ambiguous or empty levels can be removed prior to comparison, enabling selection of taxonomies with more complete taxonomic information. For example, "^[dkpcofgs]__" will recognize greengenes or silva rank handles. [optional]
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'Number of jobs to run in parallel.   [default: 1]'
           - names:
-              - --o-taxonomy-stats
-            argument: VISUALIZATION
-            description: '[required]'
+              - --o-predictions
+            argument: ARTIFACT SampleData[RegressorPredictions]
+            description: Predicted target values for each input sample.
           - names:
               - --output-dir
             argument: PATH
@@ -9533,26 +14335,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -9565,38 +14347,86 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: extract-seq-segments
-        description: Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value.
-        usage: qiime rescript extract-seq-segments [OPTIONS]
+      - name: regress-samples
+        description: Train and test a cross-validated supervised
+        usage: qiime sample-classifier regress-samples [OPTIONS]
         options:
           - names:
-              - --i-input-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences from which matching shorter sequence segments (regions) can be extracted from. Sequences containing segments that match those from 'reference-segment-sequences' will have those segments extracted and written to file. [required]
+            - --i-table
+            argument: ARTIFACT
+            description: Feature table containing all features that should be used for target prediction. [required]
           - names:
-              - --i-reference-segment-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequence segments that will be used to search for and extract matching segments from 'sequences'. [required]
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Numeric metadata column to use as prediction target. [required]
           - names:
-              - --p-perc-identity
+              - --p-test-size
             argument: PROPORTION
-            description: The percent identity at which clustering should be performed.
+            description: Fraction of input samples to exclude from training set and use for classifier testing.
           - names:
-              - --p-min-seq-len
+              - --p-step
+            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
+            description: If optimize-feature-selection is True, step is the percentage of features to remove at each iteration.
+          - names:
+              - --p-cv
             argument: INTEGER
-            description: Minimum length of sequence allowed for searching.
+            description: Number of k-fold cross-validations to perform.
           - names:
-              - --p-threads
+              - --p-random-state
             argument: INTEGER
-            description: Number of computation threads to use (1 to 256).
+            description: Seed used by random number generator. [optional]
           - names:
-              - --o-extracted-sequence-segments
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Extracted sequence segments from 'input-sequences' that succesfully aligned to 'reference-segment-sequences'. [required]
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'Number of jobs to run in parallel. [default: 1]'
           - names:
-              - --o-unmatched-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences in 'input-sequences' that did not have matching sequence segments within 'reference-segment-sequences'. [required]
+              - --p-n-estimators
+            argument: INTEGER
+            description: Number of trees to grow for estimation.
+          - names:
+              - --p-estimator
+            argument: '{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor, ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}'
+            description: Estimator method to use for sample prediction.
+          - names:
+              - --p-optimize-feature-selection
+              - --p-no-optimize-feature-selection
+            argument: ""
+            description: Automatically optimize input feature selection using recursive feature elimination.
+          - names:
+              - --p-stratify
+              - --p-no-stratify
+            argument: ""
+            description: 'Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: False]'
+          - names:
+              - --p-parameter-tuning
+              - --p-no-parameter-tuning
+            argument: ""
+            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
+          - names:
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+          - names:
+              - --o-sample-estimator
+            argument: ARTIFACT SampleEstimator[Regressor]
+            description: Trained sample estimator. [required]
+          - names:
+              - --o-feature-importance
+            argument: ARTIFACT FeatureData[Importance]
+            description: Importance of each input feature to model accuracy. [required]
+          - names:
+              - --o-predictions
+            argument: ARTIFACT SampleData[RegressorPredictions]
+            description: Predicted target values for each input sample. [required]
+          - names:
+              - --o-model-summary
+            argument: VISUALIZATION
+            description: Summarized parameter and (if enabled) feature selection information for the trained estimator. [required]
+          - names:
+              - --o-accuracy-results
+            argument: VISUALIZATION
+            description: Accuracy results visualization. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -9606,6 +14436,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -9618,34 +14468,61 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-seqs-length
-        description: Filter sequences by length.
-        usage: qiime rescript filter-seqs-length [OPTIONS]
+      - name: regress-samples-ncv
+        description: Nested cross-validated supervised learning
+        usage: qiime sample-classifier regress-samples-ncv [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences to be filtered by length. [required]
+            - --i-table
+            argument: ARTIFACT
+            description: Feature table containing all features that should be used for target prediction. [required]
           - names:
-              - --p-global-min
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Numeric metadata column to use as prediction target.
+          - names:
+              - --p-cv
             argument: INTEGER
-            description: The minimum length threshold for filtering all sequences.
+            description: Number of k-fold cross-validations to perform.
           - names:
-              - --p-global-max
+              - --p-random-state
             argument: INTEGER
-            description: The maximum length threshold for filtering all sequences.
+            description: Seed used by random number generator. [optional]
+          - names:
+              - --p-n-jobs
+            argument: NTHREADS
+            description: 'Number of jobs to run in parallel. [default: 1]'
+          - names:
+              - --p-n-estimators
+            argument: INTEGER
+            description: Number of trees to grow for estimation.
+          - names:
+              - --p-estimator
+            argument: '{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor, ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}'
+            description: Estimator method to use for sample prediction.
+          - names:
+              - --p-stratify
+              - --p-no-stratify
+            argument: ""
+            description: 'Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: False]'
+          - names:
+              - --p-parameter-tuning
+              - --p-no-parameter-tuning
+            argument: ""
+            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
           - names:
-              - --p-threads
-            argument: INTEGER
-            description: Number of computation threads to use (1 to 256).
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
           - names:
-              - --o-filtered-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences that pass the filtering thresholds.
+              - --o-predictions
+            argument: ARTIFACT SampleData[RegressorPredictions]
+            description: Predicted target values for each input sample. [required]
           - names:
-              - --o-discarded-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences that fall outside the filtering thresholds. [required]
+              - --o-feature-importance
+            argument: ARTIFACT FeatureData[Importance]
+            description: Importance of each input feature to model accuracy. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -9667,46 +14544,27 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-seqs-length-by-taxon
-        description: Filter sequences by length and taxonomic group.
-        usage: qiime rescript filter-seqs-length-by-taxon [OPTIONS]
+      - name: scatterplot
+        description: Make 2D scatterplot and linear regression of
+        usage: qiime sample-classifier scatterplot [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences to be filtered by length. [required]
-          - names:
-              - --i-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomic classifications of sequences to be filtered. [required]
-          - names:
-              - --p-labels
-            argument: TEXT...
-            description: One or more taxonomic labels to use for conditional filtering. [required]
-          - names:
-              - --p-min-lens
-            argument: INTEGERS...
-            description: Minimum length thresholds to use for filtering sequences associated with each label.
-          - names:
-              - --p-max-lens
-            argument: INTEGERS...
-            description: Maximum length thresholds to use for filtering sequences associated with each label.
-          - names:
-              - --p-global-min
-            argument: INTEGER
-            description: The minimum length threshold for filtering all sequences.
+              - --i-predictions
+            argument: ARTIFACT SampleData[RegressorPredictions]
+            description: Predicted values to plot on y axis. Must be predictions of numeric data produced by a sample regressor. [required]
           - names:
-              - --p-global-max
-            argument: INTEGER
-            description: The maximum length threshold for filtering all sequences.
+              - --m-truth-file
+              - --m-truth-column
+            argument: METADATA
+            description: Metadata column (true values) to plot on x axis.
           - names:
-              - --o-filtered-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences that pass the filtering thresholds.
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
           - names:
-              - --o-discarded-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences that fall outside the filtering thresholds. [required]
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -9728,30 +14586,52 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: filter-taxa
-        description: Filter taxonomy by list of IDs or search criteria.
-        usage: qiime rescript filter-taxa [OPTIONS]
+      - name: split-table
+        description: Split a feature table into training and testing
+        usage: qiime sample-classifier split-table [OPTIONS]
         options:
           - names:
-              - --i-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomy to filter. [required]
+              - --i-table
+            argument: ARTIFACT
+            description: Feature table containing all features that should be used for target prediction.
           - names:
-              - --m-ids-to-keep-file
-            argument: METADATA...
-            description: List of IDs to keep (as Metadata).
+              - --m-metadata-file
+              - --m-metadata-column
+            argument: METADATA
+            description: Numeric metadata column to use as prediction target.
           - names:
-              - --p-include
-            argument: TEXT...
-            description: List of search terms. Taxa containing one or more of these terms will be retained.
+              - --p-test-size
+            argument: PROPORTION
+            description: Fraction of input samples to exclude from training set and use for classifier testing.
           - names:
-              - --p-exclude
-            argument: TEXT...
-            description: List of search terms. Taxa containing one or more of these terms will be excluded.
+              - --p-random-state
+            argument: INTEGER
+            description: Seed used by random number generator. [optional]
           - names:
-              - --o-filtered-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: The filtered taxonomy. [required]
+              - --p-stratify
+              - --p-no-stratify
+            argument: ""
+            description: 'Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: True]'
+          - names:
+              - --p-missing-samples
+            argument: TEXT Choices('error', 'ignore')
+            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+          - names:
+              - --o-training-table
+            argument: ARTIFACT FeatureTable
+            description: Feature table containing training samples [required]
+          - names:
+              - --o-test-table
+            argument: ARTIFACT FeatureTable
+            description: Feature table containing test samples [required]
+          - names:
+              - --o-training-targets
+            argument: ARTIFACT SampleData[TrueTargets]
+            description: Series containing true target values of train samples
+          - names:
+              - --o-test-targets
+            argument: ARTIFACT SampleData[TrueTargets]
+            description: Series containing true target values of test samples
           - names:
               - --output-dir
             argument: PATH
@@ -9773,30 +14653,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: get-gtdb-data
-        description: Download, parse, and import SSU GTDB reference data.
-        usage: qiime rescript get-gtdb-data [OPTIONS]
+      - name: summarize
+        description: Summarize parameter and feature extraction
+        usage: qiime sample-classifier summarize [OPTIONS]
         options:
           - names:
-              - --p-version
-            argument: TEXT Choices('202.0', '207.0', '214.0', '214.1')
-            description: 'GTDB database version to download. [default: ''214.1'']'
-          - names:
-              - --p-domain
-            argument: TEXT Choices('Both', 'Bacteria', 'Archaea')
-            description: 'SSU sequence and taxonomy data to download from a given microbial domain from GTDB. ''Both'' will fetch both bacterial and archaeal data. ''Bacteria'' will only fetch bacterial data. ''Archaea'' will only fetch archaeal data. This only applies to ''db-type SpeciesReps''. [default: ''Both'']'
-          - names:
-              - --p-db-type
-            argument: TEXT Choices('All', 'SpeciesReps')
-            description: '''All'': All SSU data that pass the quality-control of GTDB, but are not clustered into representative species. ''SpeciesReps'': SSU gene sequences identified within the set of representative species. Note: if ''All'' is used, the ''domain'' parameter will be ignored as GTDB does not maintain separate domain-level files for these non-clustered data. [default: ''SpeciesReps'']'
-          - names:
-              - --o-gtdb-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: SSU GTDB reference taxonomy. [required]
+              - --i-sample-estimator
+            argument: ""
+            description: ARTIFACT SampleEstimator[Classifier | Regressor] Sample estimator trained with fit_classifier or fit_regressor. [required]
           - names:
-              - --o-gtdb-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: SSU GTDB reference sequences. [required]
+              - --o-visualization
+            argument: VISUALIZATION
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -9818,97 +14686,106 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: get-ncbi-data
-        description: Download, parse, and import NCBI sequences and taxonomies
-        usage: qiime rescript get-ncbi-data [OPTIONS]
+  - name: moshpit
+    description: QIIME 2 plugin for metagenome analysis.
+    usage: qiime moshpit [OPTIONS] COMMAND [ARGS]...
+    options:
+      - names:
+          - --version
+        argument: ""
+        description: Show the version and exit.
+      - names:
+          - --example-data
+        argument: PATH
+        description: Write example data and exit.
+      - names:
+          - --citations
+        argument: ""
+        description: Show citations and exit.
+      - names:
+          - --show-hidden-actions
+        argument: ""
+        description: This plugin has hidden actions with names starting with '_'. These are generally called internally by pipelines. Passing this flag will display those actions.
+      - names:
+          - --help
+        argument: ""
+        description: Show this message and exit.
+    subcommands:
+      - name: bin-contigs-metabat
+        description: Bin contigs into MAGs using MetaBAT 2.
+        usage: qiime moshpit bin-contigs-metabat [OPTIONS]
         options:
           - names:
-              - --p-query
-            argument: TEXT
-            description: Query on the NCBI Nucleotide database [optional]
-          - names:
-              - --m-accession-ids-file
-            argument: METADATA...
-            description: List of accession ids for sequences in the NCBI Nucleotide database.
-          - names:
-              - --p-ranks
-            argument: TEXT...
-            description: List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy database.
-          - names:
-              - --p-rank-propagation
-              - --p-no-rank-propagation
-            argument: ""
-            description: Propagate known ranks to missing ranks if true
+              - --i-contigs
+            argument: ARTIFACT
+            description: Contigs to be binned. [required]
           - names:
-              - --p-logging-level
-            argument: TEXT Choices('DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL')
-            description: Logging level
+              - --i-alignment-maps
+            argument: ARTIFACT
+            description: Reads-to-contig alignment maps. [required]
           - names:
-              - --p-n-jobs
+              - --p-min-contig
             argument: INTEGER
-            description: 'Number of concurrent download connections. More is faster until you run out of bandwidth. [default: 1]'
-          - names:
-              - --o-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences from the NCBI Nucleotide database [required]
+            description: Minimum size of a contig for binning.
           - names:
-              - --o-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomies from the NCBI Taxonomy database [required]
+              - --p-max-p
+            argument: INTEGER
+            description: Percentage of "good" contigs considered for binning decided by connection among contigs.
           - names:
-              - --output-dir
-            argument: PATH
-            description: Output unspecified results to a directory
+              - --p-min-s
+            argument: INTEGER
+            description: Minimum score of a edge for binning.
           - names:
-              - --verbose
-              - --quiet
-            argument: ""
-            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+              - --p-max-edges
+            argument: INTEGER
+            description: Maximum number of edges per node.
           - names:
-              - --example-data
-            argument: PATH
-            description: Write example data and exit.
+              - --p-p-tnf
+            argument: INTEGER
+            description: TNF probability cutoff for building TNF graph.
           - names:
-              - --citations
+              - --p-no-add
+              - --p-no-no-add
             argument: ""
-            description: Show citations and exit.
+            description: Turning off additional binning for lost or small contigs.
           - names:
-              - --help
-            argument: ""
-            description: Show this message and exit.
-      - name: get-ncbi-data-protein
-        description: Download, parse, and import NCBI protein sequences and taxonomies
-        usage: qiime rescript get-ncbi-data-protein [OPTIONS]
-        options:
+              - --p-min-cv
+            argument: INTEGER
+            description: Minimum mean coverage of a contig in each library for binning.
           - names:
-              - --p-query
-            argument: TEXT
-            description: Query on the NCBI Protein database [optional]
+              - --p-min-cv-sum
+            argument: INTEGER
+            description: Minimum total effective mean coverage of a contig (sum of depth over minCV) for binning.
           - names:
-              - --m-accession-ids-file
-            argument: METADATA...
-            description: List of accession ids for sequences in the NCBI Protein database.
+              - --p-min-cls-size
+            argument: INTEGER
+            description: Minimum size of a bin as the output. [optional]
           - names:
-              - --p-ranks
-            argument: TEXT...
-            description: List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy database.
+              - --p-seed
+            argument: INTEGER
+            description: 'For exact reproducibility. (0: use random seed)'
           - names:
-              - --p-rank-propagation
-              - --p-no-rank-propagation
+              - --p-debug
+              - --p-no-debug
+            argument: ""
+            description: Debug output. [optional]
+          - names:
+              - --p-verbose
+              - --p-no-verbose
             argument: ""
-            description: Propagate known ranks to missing ranks if true
+            description: Verbose output. [optional]
           - names:
-              - --p-n-jobs
-            argument: INTEGER
-            description: 'Number of concurrent download connections. More is faster until you run out of bandwidth. [default: 1]'
+              - --o-mags
+            argument: ARTIFACT
+            description: The resulting MAGs. [required]
           - names:
-              - --o-sequences
-            argument: ARTIFACT FeatureData[ProteinSequence]
-            description: Sequences from the NCBI Protein database [required]
+              - --o-contig-map
+            argument: ARTIFACT
+            description: Mapping of MAG identifiers to the contig identifiers contained in each MAG. [required]
           - names:
-              - --o-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomies from the NCBI Taxonomy database [required]
+              - --o-unbinned-contigs
+            argument: ARTIFACT
+            description: Contigs that were not binned into any MAG. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -9930,52 +14807,40 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: get-ncbi-genomes
-        description: Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.
-        usage: qiime rescript get-ncbi-genomes [OPTIONS]
+      - name: build-custom-diamond-db
+        description: Create a DIAMOND formatted reference database from a FASTA input file.
+        usage: qiime moshpit build-custom-diamond-db [OPTIONS]
         options:
           - names:
-              - --p-taxon
-            argument: TEXT
-            description: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank. [required]
+              - --i-seqs
+            argument: ARTIFACT
+            description: Protein reference database. [required]
           - names:
-              - --p-assembly-source
-            argument: TEXT Choices('refseq', 'genbank')
-            description: Fetch only RefSeq or GenBank genome assemblies.
+              - --i-taxonomy
+            argument: ARTIFACT
+            description: Reference taxonomy, needed to provide taxonomy features. [optional]
           - names:
-              - --p-assembly-levels
-            argument: TEXT... Choices('complete_genome', 'chromosome', 'scaffold', 'contig')
-            description: Fetch only genome assemblies that are one of the specified assembly levels.
+              - --p-threads
+            argument: INTEGER
+            description: Number of CPU threads.
           - names:
-              - --p-only-reference
-              - --p-no-only-reference
+              - --p-ignore-warnings
+              - --p-no-ignore-warnings
             argument: ""
-            description: 'Fetch only reference and representative genome assemblies. [default: True]'
+            description: 'Ignore warnings. [default: False]'
           - names:
-              - --p-tax-exact-match
-              - --p-no-tax-exact-match
+              - --p-no-parse-seqids
+              - --p-no-no-parse-seqids
             argument: ""
-            description: 'If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too. [default: False]'
+            description: 'Print raw seqids without parsing. [default: False]'
           - names:
-              - --p-page-size
-            argument: INTEGER Range(20, 1000, inclusive_end=True)
-            description: 'The maximum number of genome assemblies to return per request. If number of genomes to fetch is higher than this number, requests will be repeated until all assemblies are fetched. [default: 20]'
-          - names:
-              - --o-genome-assemblies
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Nucleotide sequences of requested genomes. [required]
+              - --p-file-buffer-size
+            argument: INTEGER
+            description: 'Range(1, None) File buffer size in bytes. [default: 67108864]'
           - names:
-              - --o-loci
+              - --o-diamond-db
             argument: ARTIFACT
-            description: Loci features of requested genomes.
-          - names:
-              - --o-proteins
-            argument: ARTIFACT GenomeData[Proteins]
-            description: Protein sequences originating from requested genomes. [required]
-          - names:
-              - --o-taxonomies
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: Taxonomies of requested genomes. [required]
+            description: DIAMOND database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -9997,33 +14862,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: get-silva-data
-        description: Download, parse, and import SILVA database.
-        usage: qiime rescript get-silva-data [OPTIONS]
+      - name: build-eggnog-diamond-db
+        description: Create a DIAMOND formatted reference database for the specified taxon.
+        usage: qiime moshpit build-eggnog-diamond-db [OPTIONS]
         options:
           - names:
-              - --p-include-species-labels
-              - --p-no-include-species-labels
-            argument: ""
-            description: 'Include species rank labels in taxonomy output. Note: species-labels may not be reliable in all cases. [default: False]'
-          - names:
-              - --p-rank-propagation
-              - --p-no-rank-propagation
-            argument: ""
-            description: 'If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for ''f__Pasteurellaceae; g__''then the ''f__'' rank will be propagated to become: ''f__Pasteurellaceae; g__Pasteurellaceae''.'
-          - names:
-              - --p-download-sequences
-              - --p-no-download-sequences
-            argument: ""
-            description: 'Toggle whether or not to download and import the SILVA reference sequences associated with the release. Skipping the sequences is useful if you only want to download and parse the taxonomy, e.g., a local copy of the sequences already exists or for testing purposes. NOTE: if this option is used, a `silva-sequences` output is still created, but contains no data. [default: True]'
+              - --i-eggnog-proteins
+            argument: ARTIFACT
+            description: eggNOG database of protein sequences and their corresponding taxonomy information (generated through the `fetch-eggnog-proteins` action). [required]
           - names:
-              - --o-silva-sequences
-            argument: ARTIFACT FeatureData[RNASequence]
-            description: SILVA reference sequences. [required]
+              - --p-taxon
+            argument: INTEGER
+            description: Taxon ID number. [required]
           - names:
-              - --o-silva-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: SILVA reference taxonomy. [required]
+              - --o-diamond-db
+            argument: ARTIFACT
+            description: Complete Diamond reference database for thespecified taxon. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -10033,26 +14887,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -10065,35 +14899,69 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: get-unite-data
-        description: Download and import UNITE reference data.
-        usage: qiime rescript get-unite-data [OPTIONS]
+      - name: build-kraken-db
+        description: Build Kraken 2 database.
+        usage: qiime moshpit build-kraken-db [OPTIONS]
         options:
           - names:
-              - --p-version
-            argument: TEXT Choices('10.0', '9.0', '8.3', '8.2')
-            description: 'UNITE version to download. [default: ''10.0'']'
+              - --i-seqs
+            argument: ARTIFACTS...
+            description: Sequences to be added to the Kraken 2 database.
           - names:
-              - --p-taxon-group
-            argument: TEXT Choices('fungi', 'eukaryotes')
-            description: 'Download a database with only ''fungi'' or including all ''eukaryotes''. [default: ''eukaryotes'']'
+              - --p-collection
+            argument: '{viral, minusb, standard, standard8, standard16, pluspf, pluspf8, pluspf16, pluspfp, pluspfp8, pluspfp16, eupathdb, nt, greengenes, rdp, silva132, silva138}'
+            description: Name of the database collection to be fetched.
           - names:
-              - --p-cluster-id
-            argument: TEXT Choices('99', '97', 'dynamic')
-            description: 'Percent similarity at which sequences in the of database were clustered. [default: ''99'']'
+              - --p-threads
+            argument: INTEGER
+            description: 'Number of threads. Only applicable when building a custom database. [default: 1]'
           - names:
-              - --p-singletons
-              - --p-no-singletons
+              - --p-kmer-len
+            argument: INTEGER
+            description: 'K-mer length in bp/aa. [default: 35]'
+          - names:
+              - --p-minimizer-len
+            argument: INTEGER
+            description: 'Minimizer length in bp/aa. [default: 31]'
+          - names:
+              - --p-minimizer-spaces
+            argument: INTEGER
+            description: Number of characters in minimizer that are ignored
+          - names:
+              - --p-max-db-size
+            argument: INTEGER
+            description: Maximum number of bytes for Kraken 2 hash table
+          - names:
+              - --p-load-factor
+            argument: PROPORTION
+            description: Proportion of the hash table to be populated.
+          - names:
+              - --p-read-len
+            argument: INTEGERS...
+            description: Ideal read lengths to be used while building the Bracken database.
+          - names:
+              - --p-no-masking
+              - --p-no-no-masking
             argument: ""
-            description: Include singleton clusters in the database.
+            description: 'Avoid masking low-complexity sequences prior to building; masking requires dustmasker or segmasker to be installed in PATH [default: False]'
           - names:
-              - --o-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: UNITE reference taxonomy. [required]
+              - --p-use-ftp
+              - --p-no-use-ftp
+            argument: ""
+            description: Use FTP for downloading instead of RSYNC.
           - names:
-              - --o-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: UNITE reference sequences. [required]
+              - --p-fast-build
+              - --p-no-fast-build
+            argument: ""
+            description: 'Do not require database to be deterministically built when using multiple threads. This is faster, but does introduce variability in minimizer/LCA pairs. [default: False]'
+          - names:
+              - --o-kraken2-database
+            argument: ARTIFACT
+            description: Kraken2DB Kraken2 database. [required]
+          - names:
+              - --o-bracken-database
+            argument: ARTIFACT
+            description: BrackenDB Bracken database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -10115,34 +14983,73 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: merge-taxa
-        description: Compare taxonomies and select the longest, highest scoring, or find the least common ancestor.
-        usage: qiime rescript merge-taxa [OPTIONS]
+      - name: classify-kaiju
+        description: Classify reads using Kaiju.
+        usage: qiime moshpit classify-kaiju [OPTIONS]
         options:
           - names:
-              - --i-data
-            argument: ARTIFACTS... List[FeatureData[Taxonomy]]
-            description: Two or more feature taxonomies to be merged.
+            - --i-seqs
+            argument: ARTIFACT
+            description: Sequences to be classified. [required]
           - names:
-              - --p-mode
-            argument: TEXT Choices('len', 'lca', 'score', 'super', 'majority')
-            description: 'How to merge feature taxonomies: "len" will select the taxonomy with the most elements (e.g., species level will beat genus level); "lca" will find the least common ancestor and report this consensus taxonomy; "score" will select the taxonomy with the highest score (e.g., confidence or consensus score). Note that "score" assumes that this score is always contained as the second column in a feature taxonomy dataframe. "majority" finds the LCA consensus while giving preference to majority labels. "super" finds the LCA consensus while giving preference to majority labels and collapsing substrings into superstrings. For example, when a more specific taxonomy does not contradict a less specific taxonomy, the more specific is chosen. That is, "g__Faecalibacterium; s__prausnitzii", will be preferred over "g__Faecalibacterium; s__" [default: ''len'']'
+              - --i-db
+            argument: ARTIFACT
+            description: Kaiju database. [required]
           - names:
-              - --p-rank-handle-regex
-            argument: TEXT
-            description: 'Regular expression indicating which taxonomic rank a label belongs to; this handle is stripped from the label prior to operating on the taxonomy. The net effect is that ambiguous or empty levels can be removed prior to comparison, enabling selection of taxonomies with more complete taxonomic information. For example, "^[dkpcofgs]__" will recognize greengenes or silva rank handles. Note that rank_handles are removed but not replaced; use the new_rank_handle parameter to replace the rank handles. [default: ''^[dkpcofgs]__'']'
+              - --p-z
+            argument: INTEGER
+            description: Number of threads.
           - names:
-              - --p-new-rank-handles
-            argument: VALUES...
-            description: Specifies the set of rank handles to prepend to taxonomic labels at each rank.
+              - --p-a
+            argument: TEXT Choices('greedy', 'mem')
+            description: 'Run mode. [default: ''greedy'']'
           - names:
-              - --p-unclassified-label
-            argument: TEXT
-            description: Specifies what label should be used for taxonomies that could not be resolved (when LCA modes are used).
+              - --p-e
+            argument: INTEGER
+            description: Number of mismatches allowed in Greedy mode.
           - names:
-              - --o-merged-data
+              - --p-m
+            argument: INTEGER
+            description: Minimum match length.
+          - names:
+              - --p-s
+            argument: INTEGER
+            description: Minimum match score in Greedy mode.
+          - names:
+              - --p-evalue
+            argument: PROPORTION
+            description: Minimum E-value in Greedy mode.
+          - names:
+              - --p-x
+              - --p-no-x
+            argument: ""
+            description: 'Enable SEG low complexity filter. [default: True]'
+          - names:
+              - --p-r
+            argument: TEXT Choices('phylum', 'class', 'order', 'family', 'genus', 'species')
+            description: Taxonomic rank.
+          - names:
+              - --p-c
+            argument: NUMBER
+            description: Minimum required number or fraction of reads for the taxon  (except viruses) to be reported.
+          - names:
+              - --p-exp
+              - --p-no-exp
+            argument: ""
+            description: Expand viruses, which are always shown as full taxon
+          - names:
+              - --p-u
+              - --p-no-u
+            argument: ""
+            description: Do not count unclassified reads for the total reads
+          - names:
+              - --o-abundances
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: Read abundances. [required]
+          - names:
+              - --o-taxonomy
             argument: ARTIFACT FeatureData[Taxonomy]
-            description: '[required]'
+            description: Linked taxonomy. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -10164,68 +15071,114 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: orient-seqs
-        description: Orient input sequences by comparison against reference.
-        usage: qiime rescript orient-seqs [OPTIONS]
+      - name: classify-kraken2
+        description: Perform taxonomic classification of reads or MAGs using Kraken 2.
+        usage: qiime moshpit classify-kraken2 [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Sequences to be oriented. [required]
+            - --i-seqs
+            argument: ARTIFACT
+            description: Sequences to be classified. [required]
           - names:
-              - --i-reference-sequences
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Reference sequences to orient against. If no reference is provided, all the sequences will be reverse complemented and all parameters will be ignored. [optional]
+              - --i-kraken2-db
+            argument: ARTIFACT Kraken 2 database.
+            description: Kraken2DB [required]
           - names:
               - --p-threads
             argument: INTEGER
-            description: Number of computation threads to use (1 to 256).
+            description: Number of threads.
           - names:
-              - --p-dbmask
-            argument: TEXT Choices('none', 'dust', 'soft')
-            description: Mask regions in the target database sequences using the dust method, or do not mask (none). When using soft masking, search commands become case sensitive.
+              - --p-confidence
+            argument: PROPORTION
+            description: 'Confidence score threshold. [default: 0.0]'
           - names:
-              - --p-relabel
-            argument: TEXT
-            description: Relabel sequences using the prefix string and a ticker (1, 2, 3, etc.) to construct the new headers. Use --sizeout to conserve the abundance annotations.
+              - --p-minimum-base-quality
+            argument: INTEGER
+            description: Minimum base quality used in classification.
           - names:
-              - --p-relabel-keep
-              - --p-no-relabel-keep
+              - --p-memory-mapping
+              - --p-no-memory-mapping
             argument: ""
-            description: When relabeling, keep the original identifier in the header after a space. [optional]
+            description: Avoids loading the database into RAM.
           - names:
-              - --p-relabel-md5
-              - --p-no-relabel-md5
+              - --p-quick
+              - --p-no-quick
             argument: ""
-            description: When relabeling, use the MD5 digest of the sequence as the new identifier. Use --sizeout to conserve the abundance annotations. [optional]
+            description: Quick operation (use first hit or hits).
           - names:
-              - --p-relabel-self
-              - --p-no-relabel-self
+              - --p-report-minimizer-data
+              - --p-no-report-minimizer-data
             argument: ""
-            description: Relabel sequences using the sequence itself as a label. [optional]
+            description: Include number of read-minimizers per-taxon and unique read-minimizers per-taxon in the repot.
+          - names:
+              - --p-minimum-hit-groups
+            argument: INTEGER
+            description: Minimum number of hit groups (overlapping k-mers sharing the same minimizer).
+          - names:
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the contigs into.
+          - names:
+              - --o-reports
+            argument: ARTIFACT
+            description: Reports produced by Kraken2. [required]
+          - names:
+              - --o-hits
+            argument: ARTIFACT
+            description: Output files produced by Kraken2. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
-              - --p-relabel-sha1
-              - --p-no-relabel-sha1
-            argument: ""
-            description: When relabeling, use the SHA1 digest of the sequence as the new identifier. The probability of a collision is smaller than the MD5 algorithm.
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-sizein
-              - --p-no-sizein
+              - --citations
             argument: ""
-            description: In de novo mode, abundance annotations (pattern `[>;]size=integer[;]`) present in sequence headers are taken into account. [optional]
+            description: Show citations and exit.
           - names:
-              - --p-sizeout
-              - --p-no-sizeout
+              - --help
             argument: ""
-            description: Add abundance annotations to the output FASTA files. [optional]
+            description: Show this message and exit.
+      - name: collate-annotations
+        description: Collate ortholog annotations.
+        usage: qiime moshpit collate-annotations [OPTIONS]
+        options:
           - names:
-              - --o-oriented-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Query sequences in same orientation as top matching reference sequence. [required]
+              - --i-ortholog-annotations
+            argument: ARTIFACTS...
+            description: Collection of ortholog annotations. [required]
           - names:
-              - --o-unmatched-seqs
-            argument: ARTIFACT FeatureData[Sequence]
-            description: Query sequences that fail to match at least one reference sequence in either + or - orientation. This will be empty if no refrence is provided.
+              - --o-collated-annotations
+            argument: ARTIFACT
+            description: FeatureData[NOG] Collated ortholog annotations. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -10247,36 +15200,51 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: parse-silva-taxonomy
-        description: Generates a SILVA fixed-rank taxonomy.
-        usage: qiime rescript parse-silva-taxonomy [OPTIONS]
+      - name: collate-busco-results
+        description: Collate BUSCO results.
+        usage: qiime moshpit collate-busco-results [OPTIONS]
         options:
           - names:
-              - --i-taxonomy-map
-            argument: ARTIFACT FeatureData[SILVATaxidMap]
-            description: 'SILVA taxonomy map. This file contains a mapping of the sequence accessions to the numeric taxonomy identifiers and species label information. The SILVA release filename is typically in the form of: ''taxmap_slv_ssu_ref_X.txt'', or ''taxmap_slv_ssu_ref_nr_X.txt'' where ''X'' is the SILVA version number. [required]'
-          - names:
-              - --i-taxonomy-ranks
-            argument: ARTIFACT FeatureData[SILVATaxonomy]
-            description: 'SILVA taxonomy file. This file contains the taxonomic rank information for each numeric taxonomy identifier and the taxonomy. The SILVA filename typically takes the form of: ''tax_slv_ssu_X.txt'', where ''X'' is the SILVA version number. [required]'
+              - --i-busco-results
+            argument: ARTIFACTS...
+            description: '[required]'
           - names:
-              - --i-taxonomy-tree
+              - --o-collated-busco-results
             argument: ARTIFACT
-            description: Phylogeny[Rooted] SILVA hierarchical taxonomy tree. The SILVA release
+            description: '[required]'
           - names:
-              - --p-rank-propagation
-              - --p-no-rank-propagation
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
             argument: ""
-            description: 'If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for ''f__Pasteurellaceae; g__''then the ''f__'' rank will be propagated to become: ''f__Pasteurellaceae; g__Pasteurellaceae''.'
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-include-species-labels
-              - --p-no-include-species-labels
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
             argument: ""
-            description: 'Include species rank labels in taxonomy output. Note: species-labels may not be reliable in all cases. [default: False]'
+            description: Show citations and exit.
           - names:
-              - --o-taxonomy
-            argument: ARTIFACT FeatureData[Taxonomy]
-            description: The resulting fixed-rank formatted SILVA taxonomy.
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: collate-feature-data-mags
+        description: Collate mags
+        usage: qiime moshpit collate-feature-data-mags [OPTIONS]
+        options:
+          - names:
+              - --i-mags
+            argument: ARTIFACTS...
+            description: A collection of MAGs to be collated. [required]
+          - names:
+              - --o-collated-mags
+            argument: ARTIFACT
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -10298,18 +15266,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: reverse-transcribe
-        description: Reverse transcribe RNA to DNA sequences.
-        usage: qiime rescript reverse-transcribe [OPTIONS]
+      - name: collate-kraken2-outputs
+        description: Collate kraken2 outputs
+        usage: qiime moshpit collate-kraken2-outputs [OPTIONS]
         options:
           - names:
-              - --i-rna-sequences
-            argument: ARTIFACT FeatureData
-            description: RNA Sequences to reverse transcribe to DNA. [required]
+              - --i-kraken2-outputs
+            argument: ARTIFACTS...
+            description: '[required]'
           - names:
-              - --o-dna-sequences
-            argument: ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]
-            description: Reverse-transcribed DNA sequences. [required]
+              - --o-collated-kraken2-outputs
+            argument: ARTIFACTS...
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -10331,18 +15299,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: subsample-fasta
-        description: Subsample an indicated number of sequences from a FASTA file.
-        usage: qiime rescript subsample-fasta [OPTIONS]
+      - name: collate-kraken2-reports
+        description: Collate kraken2 reports
+        usage: qiime moshpit collate-kraken2-reports [OPTIONS]
         options:
           - names:
-              - --i-sequences
-            argument: ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]
-            description: Sequences to subsample from. [required]
+              - --i-kraken2-reports
+            argument: ARTIFACTS...
+            description: '[required]'
           - names:
-              - --o-sample-sequences
-            argument: ARTIFACT FeatureData[AlignedSequence¹ | Sequence²]
-            description: Sample of original sequences. [required]
+              - --o-collated-kraken2-reports
+            argument: ARTIFACTS...
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -10364,34 +15332,18 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: trim-alignment
-        description: Trim alignment based on provided primers or specific positions.
-        usage: qiime rescript trim-alignment [OPTIONS]
+      - name: collate-orthologs
+        description: Collate Orthologs
+        usage: qiime moshpit collate-orthologs [OPTIONS]
         options:
           - names:
-              - --i-aligned-sequences
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: Aligned DNA sequences. [required]
-          - names:
-              - --p-primer-fwd
-            argument: TEXT
-            description: Forward primer used to find the start position for alignment trimming. [optional]
-          - names:
-              - --p-primer-rev
-            argument: TEXT
-            description: Reverse primer used to find the end position for alignment trimming. [optional]
-          - names:
-              - --p-position-start
-            argument: INTEGER
-            description: Position within the alignment where the trimming will begin.
-          - names:
-              - --p-position-end
-            argument: INTEGER
-            description: Position within the alignment where the trimming will end.
+              - --i-orthologs
+            argument: ARTIFACTS...
+            description: Orthologs to collate [required]
           - names:
-              - --o-trimmed-sequences
-            argument: ARTIFACT FeatureData[AlignedSequence]
-            description: Trimmed sequence alignment. [required]
+              - --o-collated-orthologs
+            argument: ARTIFACT
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -10402,25 +15354,38 @@ subcommands:
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --no-recycle
+              - --citations
             argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+            description: Show citations and exit.
           - names:
-              - --parallel
+              - --help
             argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
+            description: Show this message and exit.
+      - name: collate-sample-data-mags
+        description: Collate mags
+        usage: qiime moshpit collate-sample-data-mags [OPTIONS]
+        options:
           - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
+              - --i-mags
+            argument: ARTIFACTS...
+            description: A collection of MAGs to be collated. [required]
           - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+              - --o-collated-mags
+            argument: ARTIFACT
+            description: SampleData[MAGs] [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
               - --example-data
             argument: PATH
@@ -10433,122 +15398,80 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-  - name: sample-classifier
-    description: Plugin for machine learning prediction of sample
-    usage: qiime sample-classifier [OPTIONS] COMMAND [ARGS]...
-    options:
-      - names:
-          - --version
-        argument: ""
-        description: Show the version and exit.
-      - names:
-          - --example-data
-        argument: PATH
-        description: Write example data and exit.
-      - names:
-          - --citations
-        argument: ""
-        description: Show citations and exit.
-      - names:
-          - --help
-        argument: ""
-        description: Show this message and exit.
-    subcommands:
-      - name: classify-samples
-        description: Train and test a cross-validated supervised
-        usage: qiime sample-classifier classify-samples [OPTIONS]
+      - name: dereplicate-mags
+        description: Dereplicate MAGs from multiple samples.
+        usage: qiime moshpit dereplicate-mags [OPTIONS]
         options:
           - names:
-              - --i-table
+              - --i-mags
             argument: ARTIFACT
-            description: Feature table containing all features that should be used for target prediction. [required]
+            description: MAGs to be dereplicated. [required]
           - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Categorical metadata column to use as prediction target. [required]
+              - --i-distance-matrix
+            argument: ARTIFACT
+            description: Matrix of distances between MAGs. [required]
           - names:
-              - --p-test-size
+              - --p-threshold
             argument: PROPORTION
-            description: Fraction of input samples to exclude from training set and use for classifier testing.
-          - names:
-              - --p-step
-            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
-            description: If optimize-feature-selection is True, step is the percentage of features to remove at each iteration.
-          - names:
-              - --p-cv
-            argument: INTEGER
-            description: Number of k-fold cross-validations to perform.
-          - names:
-              - --p-random-state
-            argument: INTEGER
-            description: Seed used by random number generator. [optional]
-          - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'Number of jobs to run in parallel. [default: 1]'
+            description: 'Similarity threshold required to consider two bins identical. [default: 0.99]'
           - names:
-              - --p-n-estimators
-            argument: INTEGER
-            description: Number of trees to grow for estimation.
+              - --o-dereplicated-mags
+            argument: ARTIFACT
+            description: Dereplicated MAGs. [required]
           - names:
-              - --p-estimator
-            argument: '{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}'
-            description: Estimator method to use for sample prediction.
+              - --o-feature-table
+            argument: ARTIFACT
+            description: Mapping between MAGs and samples. [required]
           - names:
-              - --p-optimize-feature-selection
-              - --p-no-optimize-feature-selection
-            argument: ""
-            description: Automatically optimize input feature selection using recursive feature elimination.
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-parameter-tuning
-              - --p-no-parameter-tuning
+              - --verbose
+              - --quiet
             argument: ""
-            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
-          - names:
-              - --p-palette
-            argument: TEXT
-            description: The color palette to use for plotting.
-          - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
-          - names:
-              - --o-sample-estimator
-            argument: ARTIFACT SampleEstimator[Classifier]
-            description: Trained sample estimator. [required]
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --o-feature-importance
-            argument: ARTIFACT FeatureData[Importance]
-            description: Importance of each input feature to model accuracy.
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --o-predictions
-            argument: ARTIFACT SampleData[ClassifierPredictions]
-            description: Predicted target values for each input sample.
+              - --citations
+            argument: ""
+            description: Show citations and exit.
           - names:
-              - --o-model-summary
-            argument: VISUALIZATION
-            description: Summarized parameter and (if enabled) feature selection information for the trained estimator.
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: eggnog-annotate
+        description: Annotate orthologs against eggNOG database
+        usage: qiime moshpit eggnog-annotate [OPTIONS]
+        options:
           - names:
-              - --o-accuracy-results
-            argument: VISUALIZATION
-            description: Accuracy results visualization. [required]
+              - --i-eggnog-hits
+            argument: ARTIFACT
+            description: SampleData[BLAST6] BLAST6-like table(s) describing the identified orthologs. [required]
           - names:
-              - --o-probabilities
-            argument: ARTIFACT SampleData[Probabilities]
-            description: Predicted class probabilities for each input sample. [required]
+              - --i-eggnog-db
+            argument: ARTIFACT
+            description: eggNOG annotation database. [required]
           - names:
-              - --o-heatmap
-            argument: VISUALIZATION
-            description: A heatmap of the top 50 most important features from the table. [required]
+              - --p-db-in-memory
+              - --p-no-db-in-memory
+            argument: ""
+            description: 'Read eggnog database into memory. The eggnog database is very large(>44GB), so this option should only be used on clusters or other machines with enough memory. [default: False]'
           - names:
-              - --o-training-targets
-            argument: ARTIFACT SampleData[TrueTargets]
-            description: Series containing true target values of train samples [required]
+              - --p-num-cpus
+            argument: INTEGER
+            description: Number of CPUs to utilize. '0' will use all available.
           - names:
-              - --o-test-targets
-            argument: ARTIFACT SampleData[TrueTargets]
-            description: Series containing true target values of test samples [required]
+              - --p-num-partitions
+            argument: INTEGER
+            description: Range(1, None) The number of partitions to split the contigs into.
+          - names:
+              - --o-ortholog-annotations
+            argument: ARTIFACT
+            description: Annotated hits. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -10590,47 +15513,39 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: classify-samples-from-dist
-        description: Run k-nearest-neighbors on a labeled distance
-        usage: qiime sample-classifier classify-samples-from-dist [OPTIONS]
+      - name: eggnog-diamond-search
+        description: Run eggNOG search using diamond aligner
+        usage: qiime moshpit eggnog-diamond-search [OPTIONS]
         options:
           - names:
-              - --i-distance-matrix
+              - --i-sequences
             argument: ARTIFACT
-            description: DistanceMatrix a distance matrix [required]
+            description: Sequence data of the contigs we want to search for hits using the Diamond Database [required]
           - names:
-              - --p-k
-            argument: INTEGER
-            description: 'Number of nearest neighbors [default: 1]'
+              - --i-diamond-db
+            argument: ARTIFACT
+            description: The filepath to an artifact containing the Diamond database [required]
           - names:
-              - --p-cv
+              - --p-num-cpus
             argument: INTEGER
-            description: Number of k-fold cross-validations to perform.
-          - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: Number of jobs to run in parallel.
-          - names:
-              - --p-palette
-            argument: TEXT
-            description: The color palette to use for plotting.
+            description: 'Number of CPUs to utilize. ''0'' will use all available. [default: 1]'
           - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Categorical metadata column to use as prediction target. [required]
+              - --p-db-in-memory
+              - --p-no-db-in-memory
+            argument: ""
+            description: Read database into memory. The database can be very large, so this option should only be used on clusters or other machines with enough memory.
           - names:
-              - --p-random-state
+              - --p-num-partitions
             argument: INTEGER
-            description: Seed used by random number generator. [optional]
+            description: The number of partitions to split the contigs into.
           - names:
-              - --o-predictions
-            argument: ARTIFACT SampleData[ClassifierPredictions]
-            description: leave one out predictions for each sample [required]
+              - --o-table
+            argument: ARTIFACT
+            description: '[required]'
           - names:
-              - --o-accuracy-results
-            argument: VISUALIZATION
-            description: Accuracy results visualization. [required]
+              - --o-eggnog-hits
+            argument: ARTIFACT
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -10672,60 +15587,42 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: classify-samples-ncv
-        description: Nested cross-validated supervised learning
-        usage: qiime sample-classifier classify-samples-ncv [OPTIONS]
+      - name: estimate-bracken
+        description: Perform read abundance re-estimation using Bracken.
+        usage: qiime moshpit estimate-bracken [OPTIONS]
         options:
           - names:
-            - --i-table
-            argument: ARTIFACT
-            description: Feature table containing all features that should be used for target prediction. [required]
-          - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Categorical metadata column to use as prediction target. [required]
+              - --i-kraken-reports
+            argument: ARTIFACT SampleData
+            description: Reports produced by Kraken2. [required]
           - names:
-              - --p-cv
-            argument: INTEGER
-            description: Number of k-fold cross-validations to perform.
+              - --i-bracken-db
+            argument: ARTIFACT
+            description: BrackenDB Bracken database. [required]
           - names:
-              - --p-random-state
+              - --p-threshold
             argument: INTEGER
-            description: Seed used by random number generator. [optional]
+            description: 'Bracken: number of reads required PRIOR to abundance estimation to perform re-estimation.'
           - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'Number of jobs to run in parallel. [default: 1]'
-          - names:
-              - --p-n-estimators
+              - --p-read-len
             argument: INTEGER
-            description: Number of trees to grow for estimation.
-          - names:
-              - --p-estimator
-            argument: '{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}'
-            description: Estimator method to use for sample prediction.
-          - names:
-              - --p-parameter-tuning
-              - --p-no-parameter-tuning
-            argument: ""
-            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
+            description: 'Bracken: read length to get all classifications for.'
           - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+              - --p-level
+            argument: TEXT Choices('D', 'P', 'C', 'O', 'F', 'G', 'S')
+            description: 'Bracken: taxonomic level to estimate abundance at.'
           - names:
-              - --o-predictions
-            argument: ARTIFACT SampleData[ClassifierPredictions]
-            description: Predicted target values for each input sample.
+              - --o-taxonomy
+            argument: ARTIFACT FeatureData[Taxonomy]
+            description: '[required]'
           - names:
-              - --o-feature-importance
-            argument: ARTIFACT FeatureData[Importance]
-            description: Importance of each input feature to model accuracy.
+              - --o-table
+            argument: ARTIFACT FeatureTable[Frequency]
+            description: '[required]'
           - names:
-              - --o-probabilities
-            argument: ARTIFACT SampleData[Probabilities]
-            description: Predicted class probabilities for each input sample.
+              - --o-reports
+            argument: ARTIFACT SampleData[Kraken2Report % Properties('bracken')]
+            description: Reports modified by Bracken. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -10747,31 +15644,110 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: confusion-matrix
-        description: Make a confusion matrix from sample classifier
-        usage: qiime sample-classifier confusion-matrix [OPTIONS]
+      - name: evaluate-busco
+        description: Evaluate quality of the generated MAGs using BUSCO.
+        usage: qiime moshpit evaluate-busco [OPTIONS]
         options:
           - names:
-              - --i-predictions
-            argument: ARTIFACT SampleData[ClassifierPredictions]
-            description: Predicted values to plot on x axis. Should be predictions of categorical data produced by a sample classifier. [required]
+              - --i-bins
+            argument: ARTIFACT
+            description: MAGs to be analyzed. [required]
           - names:
-              - --i-probabilities
-            argument: ARTIFACT SampleData[Probabilities]
-            description: Predicted class probabilities for each input sample.
+              - --p-mode
+            argument: TEXT
+            description: Specify which BUSCO analysis mode to run.
           - names:
-              - --m-truth-file
-              - --m-truth-column
-            argument: METADATA
-            description: Metadata column (true values) to plot on y axis.
+              - --p-lineage-dataset
+            argument: TEXT
+            description: Specify the name of the BUSCO lineage to be used. To see all possible options run `busco --list-datasets`. [optional]
           - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+              - --p-augustus
+              - --p-no-augustus
+            argument: ""
+            description: Use augustus gene predictor for eukaryote runs.
+          - names:
+              - --p-augustus-parameters
+            argument: TEXT
+            description: 'Pass additional arguments to Augustus. All arguments should be contained within a single string with no white space, with each argument separated by a comma. Example: ''--PARAM1=VALUE1,--PARAM2=VALUE2''.'
+          - names:
+              - --p-augustus-species
+            argument: TEXT
+            description: Specify a species for Augustus training. [optional]
+          - names:
+              - --p-auto-lineage
+              - --p-no-auto-lineage
+            argument: ""
+            description: Run auto-lineage to find optimum lineage path.
+          - names:
+              - --p-auto-lineage-euk
+              - --p-no-auto-lineage-euk
+            argument: ""
+            description: 'Run auto-placement just on eukaryote tree to find optimum lineage path. [default: False]'
+          - names:
+              - --p-auto-lineage-prok
+              - --p-no-auto-lineage-prok
+            argument: ""
+            description: 'Run auto-lineage just on non-eukaryote trees to find optimum lineage path. [default: False]'
+          - names:
+              - --p-cpu
+            argument: INTEGER
+            description: Specify the number (N=integer) of threads/cores to use.
+          - names:
+              - --p-config
+            argument: TEXT
+            description: Provide a config file. [optional]
+          - names:
+              - --p-contig-break
+            argument: INTEGER
+            description: Number of contiguous Ns to signify a break between contigs.
+          - names:
+              - --p-evalue
+            argument: NUMBER
+            description: 'E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03, Default: 1e-03. [default: 0.001]'
+          - names:
+              - --p-force
+              - --p-no-force
+            argument: ""
+            description: 'Force rewriting of existing files. Must be used when output files with the provided name already exist. [default: False]'
+          - names:
+              - --p-limit
+            argument: INTEGER
+            description: How many candidate regions (contig or transcript) to consider per BUSCO.
+          - names:
+              - --p-long
+              - --p-no-long
+            argument: ""
+            description: 'Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms.'
+          - names:
+              - --p-metaeuk-parameters
+            argument: TEXT
+            description: 'Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single string with no white space, with each argument separated by a comma. Example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. [optional]'
+          - names:
+              - --p-metaeuk-rerun-parameters
+            argument: TEXT
+            description: 'Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma. Example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. [optional]'
+          - names:
+              - --p-miniprot
+              - --p-no-miniprot
+            argument: ""
+            description: Use miniprot gene predictor for eukaryote runs.
+          - names:
+              - --p-scaffold-composition
+              - --p-no-scaffold-composition
+            argument: ""
+            description: 'Writes ACGTN content per scaffold to a file `scaffold_composition.txt`. [default: False]'
+          - names:
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the contigs into.
+          - names:
+              - --o-results-table
+            argument: ARTIFACT
+            description: BUSCO result table. [required]
           - names:
               - --o-visualization
             argument: VISUALIZATION
-            description: '[required]'
+            description: Visualization of the BUSCO results. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -10781,6 +15757,26 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
+          - names:
+              - --recycle-pool
+            argument: TEXT
+            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+          - names:
+              - --no-recycle
+            argument: ""
+            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+          - names:
+              - --parallel
+            argument: ""
+            description: Execute your action in parallel. This flag will use your default parallel config.
+          - names:
+              - --parallel-config
+            argument: FILE
+            description: Execute your action in parallel using a config at the indicated path.
+          - names:
+              - --use-cache
+            argument: DIRECTORY
+            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -10793,65 +15789,14 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: fit-classifier
-        description: Fit a supervised learning classifier.
-        usage: qiime sample-classifier fit-classifier [OPTIONS]
+      - name: fetch-diamond-db
+        description: Fetch the complete Diamond database necessary to run the eggnog-diamond-search action.
+        usage: qiime moshpit fetch-diamond-db [OPTIONS]
         options:
           - names:
-            - --i-table
-            argument: ARTIFACT
-            description: Feature table containing all features that should be used for target prediction. [required]
-          - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Numeric metadata column to use as prediction target.
-          - names:
-              - --p-step
-            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
-            description: If optimize-feature-selection is True, step is the percentage of features to remove at each iteration. [required]
-          - names:
-              - --p-cv
-            argument: INTEGER
-            description: Number of k-fold cross-validations to perform.
-          - names:
-              - --p-random-state
-            argument: INTEGER
-            description: Seed used by random number generator. [optional]
-          - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'Number of jobs to run in parallel. [default: 1]'
-          - names:
-              - --p-n-estimators
-            argument: INTEGER
-            description: Number of trees to grow for estimation.
-          - names:
-              - --p-estimator
-            argument: '{RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, AdaBoostClassifier[DecisionTree], AdaBoostClassifier[ExtraTrees], KNeighborsClassifier, LinearSVC, SVC}'
-            description: Estimator method to use for sample prediction.
-          - names:
-              - --p-optimize-feature-selection
-              - --p-no-optimize-feature-selection
-            argument: ""
-            description: 'Automatically optimize input feature selection using recursive feature elimination. [default: False]'
-          - names:
-              - --p-parameter-tuning
-              - --p-no-parameter-tuning
-            argument: ""
-            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
-          - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
-          - names:
-              - --o-sample-estimator
-            argument: ARTIFACT SampleEstimator[Classifier]
-            description: Trained sample classifier. [required]
-          - names:
-              - --o-feature-importance
-            argument: ARTIFACT FeatureData[Importance]
-            description: Importance of each input feature to model accuracy. [required]
+              - --o-diamond-db
+            argument: ARTIFACT
+            description: Complete Diamond reference database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -10873,65 +15818,76 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: fit-regressor
-        description: Fit a supervised learning regressor.
-        usage: qiime sample-classifier fit-regressor [OPTIONS]
+      - name: fetch-eggnog-db
+        description: Fetch the databases necessary to run the eggnog-annotate action.
+        usage: qiime moshpit fetch-eggnog-db [OPTIONS]
         options:
           - names:
-            - --i-table
+              - --o-eggnog-db
             argument: ARTIFACT
-            description: Feature table containing all features that should be used for target prediction. [required]
+            description: Artifact containing the eggNOG annotation database. [required]
           - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Numeric metadata column to use as prediction target. [required]
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-step
-            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
-            description: If optimize-feature-selection is True, step is the percentage of features to remove at each iteration.
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-cv
-            argument: INTEGER
-            description: Number of k-fold cross-validations to perform.
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-random-state
-            argument: INTEGER
-            description: Seed used by random number generator. [optional]
+              - --citations
+            argument: ""
+            description: Show citations and exit.
           - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'Number of jobs to run in parallel. [default: 1]'
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: fetch-eggnog-proteins
+        description: Fetch the databases necessary to run the build-eggnog-diamond-db action.
+        usage: qiime moshpit fetch-eggnog-proteins [OPTIONS]
+        options:
           - names:
-              - --p-n-estimators
-            argument: INTEGER
-            description: Number of trees to grow for estimation.
+              - --o-eggnog-proteins
+            argument: ARTIFACT
+            description: eggNOG database of protein sequences and their corresponding taxonomy information. [required]
           - names:
-              - --p-estimator
-            argument: '{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor[DecisionTree], AdaBoostRegressor[ExtraTrees], ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}'
-            description: Estimator method to use for sample prediction.
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-optimize-feature-selection
-              - --p-no-optimize-feature-selection
+              - --verbose
+              - --quiet
             argument: ""
-            description: 'Automatically optimize input feature selection using recursive feature elimination. [default: False]'
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-parameter-tuning
-              - --p-no-parameter-tuning
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
+          - names:
+              - --citations
             argument: ""
-            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
+            description: Show citations and exit.
           - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: How to handle missing samples in metadata.
+              - --help
+            argument: ""
+            description: Show this message and exit.
+      - name: fetch-kaiju-db
+        description: Fetch Kaiju database.
+        usage: qiime moshpit fetch-kaiju-db [OPTIONS]
+        options:
           - names:
-              - --o-sample-estimator
-            argument: ARTIFACT SampleEstimator[Regressor]
-            description: 'Trained sample regressor. [required]'
+              - --p-database-type
+            argument: '{nr, nr_euk, refseq, fungi, viruses, plasmids, progenomes, rvdb}'
+            description: Type of database to be downloaded. [required]
           - names:
-              - --o-feature-importance
-            argument: ARTIFACT FeatureData[Importance]
-            description: Importance of each input feature to model accuracy. [required]
+              - --o-database
+            argument: ARTIFACT
+            description: Kaiju database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -10953,74 +15909,60 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: heatmap
-        description: Generate heatmap of important features.
-        usage: qiime sample-classifier heatmap [OPTIONS]
+      - name: fetch-ncbi-taxonomy
+        description: Fetch NCBI reference taxonomy
+        usage: qiime moshpit fetch-ncbi-taxonomy [OPTIONS]
         options:
           - names:
-            - --i-table
+              - --o-taxonomy
             argument: ARTIFACT
-            description: Feature table containing all features that should be used for target prediction. [required]
-          - names:
-              - --i-importance
-            argument: ARTIFACT FeatureData[Importance]
-            description: Feature importances. [required]
-          - names:
-              - --m-sample-metadata-file
-              - --m-sample-metadata-column
-            argument: METADATA
-            description: Sample metadata column to use for sample labeling or grouping. [optional]
+            description: NCBI reference taxonomy. [required]
           - names:
-              - --m-feature-metadata-file
-              - --m-feature-metadata-column
-            argument: METADATA
-            description: Feature metadata (e.g., taxonomy) to use for labeling features in the heatmap. [optional]
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
           - names:
-              - --p-feature-count
-            argument: INTEGER
-            description: Filter feature table to include top N most important features.
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --p-importance-threshold
-            argument: NUMBER
-            description: Filter feature table to include top N most important features.
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --p-group-samples
-              - --p-no-group-samples
+              - --citations
             argument: ""
-            description: 'Group samples by sample metadata. [default: False]'
+            description: Show citations and exit.
           - names:
-              - --p-normalize
-              - --p-no-normalize
+              - --help
             argument: ""
-            description: Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table.
-          - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''ignore'']'
-          - names:
-              - --p-metric
-            argument: TEXT
-            description: Metrics exposed by seaborn
+            description: Show this message and exit.
+      - name: filter-derep-mags
+        description: Filter dereplicated MAGs.
+        usage: qiime moshpit filter-derep-mags [OPTIONS]
+        options:
           - names:
-              - --p-method
-            argument: TEXT
-            description: Clustering methods exposed by seaborn
+              - --i-mags
+            argument: ARTIFACT
+            description: Dereplicated MAGs to filter. [required]
           - names:
-              - --p-cluster
-            argument: TEXT Choices('both', 'features', 'none', 'samples')
-            description: 'Specify which axes to cluster. [default: ''features'']'
+              - --m-metadata-file
+            argument: METADATA...
+            description: Sample metadata indicating which MAG ids to filter. [required]
           - names:
-              - --p-color-scheme
+              - --p-where
             argument: TEXT
-            description: Color scheme for heatmap.
+            description: Optional SQLite WHERE clause specifying MAG metadata criteria that must be met to be included in the filtered data. If not provided, all MAGs in `metadata` that are also in the MAG data will be retained.
           - names:
-              - --o-heatmap
-            argument: VISUALIZATION
-            description: Heatmap of important features. [required]
+              - --p-exclude-ids
+              - --p-no-exclude-ids
+            argument: ""
+            description: 'Defaults to False. If True, the MAGs selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]'
           - names:
-              - --o-filtered-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Filtered feature table containing data displayed in heatmap. [required]
+              - --o-filtered-mags
+            argument: ARTIFACT
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -11030,26 +15972,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -11062,35 +15984,39 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: metatable
-        description: Convert (and merge) positive numeric metadata
-        usage: qiime sample-classifier metatable [OPTIONS]
+      - name: filter-mags
+        description: Filter MAGs.
+        usage: qiime moshpit filter-mags [OPTIONS]
         options:
           - names:
-              - --i-table
+              - --i-mags
             argument: ARTIFACT
-            description: Feature table containing all features that should be used for target prediction.
+            description: MAGs to filter. [required]
           - names:
               - --m-metadata-file
             argument: METADATA...
-            description: Metadata file to convert to feature table. [required]
-          - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''ignore'']'
+            description: Sample metadata indicating which MAG ids to filter. [required]
           - names:
-              - --p-missing-values
-            argument: TEXT Choices('drop_samples', 'drop_features', 'error', 'fill')
-            description: How to handle missing values (nans) in metadata.
+              - --p-where
+            argument: TEXT
+            description: Optional SQLite WHERE clause specifying MAG metadata criteria that must be met to be included in the filtered data. If not provided, all MAGs in `metadata` that are also in the MAG data will be retained.
           - names:
-              - --p-drop-all-unique
-              - --p-no-drop-all-unique
+              - --p-exclude-ids
+              - --p-no-exclude-ids
             argument: ""
-            description: 'If True, columns that contain a unique value for every ID will be dropped. [default: False]'
+            description: 'Defaults to False. If True, the MAGs selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]'
           - names:
-              - --o-converted-table
-            argument: ARTIFACT FeatureTable[Frequency]
-            description: Converted feature table [required]
+              - --p-on
+            argument: TEXT Choices('sample', 'mag')
+            description: Whether to filter based on sample or MAG metadata.
+          - names:
+              - --m-metadata-file
+            argument: METADATA...
+            description: (multiple Sample metadata indicating which MAG ids to filter.
+          - names:
+              - --o-filtered-mags
+            argument: ARTIFACT
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -11101,25 +16027,38 @@ subcommands:
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
+              - --example-data
+            argument: PATH
+            description: Write example data and exit.
           - names:
-              - --no-recycle
+              - --citations
             argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
+            description: Show citations and exit.
           - names:
-              - --parallel
+              - --help
             argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
+            description: Show this message and exit.
+      - name: get-feature-lengths
+        description: Get feature lengths.
+        usage: qiime moshpit get-feature-lengths [OPTIONS]
+        options:
           - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
+              - --i-features
+            argument: ARTIFACT
+            description: Features to get lengths for. [required]
           - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
+              - --o-lengths
+            argument: ARTIFACT
+            description:  Feature lengths. [required]
+          - names:
+              - --output-dir
+            argument: PATH
+            description: Output unspecified results to a directory
+          - names:
+              - --verbose
+              - --quiet
+            argument: ""
+            description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
           - names:
               - --example-data
             argument: PATH
@@ -11132,26 +16071,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: predict-classification
-        description: Use trained classifier to predict target values
-        usage: qiime sample-classifier predict-classification [OPTIONS]
+      - name: inspect-kraken2-db
+        description: Inspect a Kraken 2 database.
+        usage: qiime moshpit inspect-kraken2-db [OPTIONS]
         options:
           - names:
-              - --i-sample-estimator
-            argument: ARTIFACT SampleEstimator[Classifier]
-            description: Sample classifier trained with fit_classifier.
-          - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'Number of jobs to run in parallel.   [default: 1]'
+              - --i-db
+            argument: ARTIFACT
+            description: The Kraken 2 database for which to generate the report. [required]
           - names:
-              - --o-predictions
-            argument: ARTIFACT SampleData[ClassifierPredictions]
-            description: Predicted target values for each input sample.
+              - --p-threads
+            argument: INTEGER
+            description: 'The number of threads to use.   Range(1, None) [default: 1]'
           - names:
-              - --o-probabilities
-            argument: ARTIFACT SampleData[Probabilities]
-            description: Predicted class probabilities for each input sample.
+              - --o-report
+            argument: ARTIFACT
+            description: The report of the supplied database. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -11173,22 +16108,26 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: predict-regression
-        description: Use trained regressor to predict target values
-        usage: qiime sample-classifier predict-regression [OPTIONS]
+      - name: kraken2-to-features
+        description: Select downstream features from Kraken 2
+        usage: qiime moshpit kraken2-to-features [OPTIONS]
         options:
           - names:
-              - --i-sample-estimator
-            argument: ARTIFACT SampleEstimator[Regressor]
-            description: Sample regressor trained with fit_regressor. [required]
+              - --i-reports
+            argument: ARTIFACT
+            description: Per-sample Kraken 2 reports. [required]
           - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'Number of jobs to run in parallel.   [default: 1]'
+              - --p-coverage-threshold
+            argument: NUMBER
+            description: 'The minimum percent coverage required to produce a feature. [default: 0.1]'
           - names:
-              - --o-predictions
-            argument: ARTIFACT SampleData[RegressorPredictions]
-            description: Predicted target values for each input sample.
+              - --o-table
+            argument: ARTIFACT
+            description: A presence/absence table of selected features. The features are not of even ranks, but will be the most specific rank available. [required]
+          - names:
+              - --o-taxonomy
+            argument: ARTIFACT
+            description: Infra-clade ranks are ignored unless they are strain-level. Missing internal ranks are annotated by their next most specific rank, with the exception of k__Bacteria and k__Archaea which match their domain's name. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -11210,86 +16149,26 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: regress-samples
-        description: Train and test a cross-validated supervised
-        usage: qiime sample-classifier regress-samples [OPTIONS]
+      - name: kraken2-to-mag-features
+        description: Select downstream MAG features from Kraken 2
+        usage: qiime moshpit kraken2-to-mag-features [OPTIONS]
         options:
           - names:
-            - --i-table
+              - --i-reports
             argument: ARTIFACT
-            description: Feature table containing all features that should be used for target prediction. [required]
-          - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Numeric metadata column to use as prediction target. [required]
-          - names:
-              - --p-test-size
-            argument: PROPORTION
-            description: Fraction of input samples to exclude from training set and use for classifier testing.
-          - names:
-              - --p-step
-            argument: PROPORTION Range(0.0, 1.0, inclusive_start=False)
-            description: If optimize-feature-selection is True, step is the percentage of features to remove at each iteration.
-          - names:
-              - --p-cv
-            argument: INTEGER
-            description: Number of k-fold cross-validations to perform.
-          - names:
-              - --p-random-state
-            argument: INTEGER
-            description: Seed used by random number generator. [optional]
-          - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'Number of jobs to run in parallel. [default: 1]'
-          - names:
-              - --p-n-estimators
-            argument: INTEGER
-            description: Number of trees to grow for estimation.
-          - names:
-              - --p-estimator
-            argument: '{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor, ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}'
-            description: Estimator method to use for sample prediction.
-          - names:
-              - --p-optimize-feature-selection
-              - --p-no-optimize-feature-selection
-            argument: ""
-            description: Automatically optimize input feature selection using recursive feature elimination.
-          - names:
-              - --p-stratify
-              - --p-no-stratify
-            argument: ""
-            description: 'Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: False]'
-          - names:
-              - --p-parameter-tuning
-              - --p-no-parameter-tuning
-            argument: ""
-            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
-          - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
-          - names:
-              - --o-sample-estimator
-            argument: ARTIFACT SampleEstimator[Regressor]
-            description: Trained sample estimator. [required]
-          - names:
-              - --o-feature-importance
-            argument: ARTIFACT FeatureData[Importance]
-            description: Importance of each input feature to model accuracy. [required]
+            description: Per-sample Kraken 2 reports. [required]
           - names:
-              - --o-predictions
-            argument: ARTIFACT SampleData[RegressorPredictions]
-            description: Predicted target values for each input sample. [required]
+              - --i-hits
+            argument: ARTIFACT
+            description: Per-sample Kraken 2 output files. [required]
           - names:
-              - --o-model-summary
-            argument: VISUALIZATION
-            description: Summarized parameter and (if enabled) feature selection information for the trained estimator. [required]
+              - --p-coverage-threshold
+            argument: NUMBER
+            description: 'The minimum percent coverage required to produce a feature. [default: 0.1]'
           - names:
-              - --o-accuracy-results
-            argument: VISUALIZATION
-            description: Accuracy results visualization. [required]
+              - --o-taxonomy
+            argument: ARTIFACT
+            description: Infra-clade ranks are ignored unless they are strain-level. Missing internal ranks are annotated by their next most specific rank, with the exception of k__Bacteria and k__Archaea which match their domain's name. [required]
           - names:
               - --output-dir
             argument: PATH
@@ -11299,26 +16178,6 @@ subcommands:
               - --quiet
             argument: ""
             description: Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).
-          - names:
-              - --recycle-pool
-            argument: TEXT
-            description: 'Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using.'
-          - names:
-              - --no-recycle
-            argument: ""
-            description: Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling.
-          - names:
-              - --parallel
-            argument: ""
-            description: Execute your action in parallel. This flag will use your default parallel config.
-          - names:
-              - --parallel-config
-            argument: FILE
-            description: Execute your action in parallel using a config at the indicated path.
-          - names:
-              - --use-cache
-            argument: DIRECTORY
-            description: 'Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/<uname> will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster.'
           - names:
               - --example-data
             argument: PATH
@@ -11331,61 +16190,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: regress-samples-ncv
-        description: Nested cross-validated supervised learning
-        usage: qiime sample-classifier regress-samples-ncv [OPTIONS]
+      - name: partition-feature-data-mags
+        description: Partition MAGs
+        usage: qiime moshpit partition-feature-data-mags [OPTIONS]
         options:
           - names:
-            - --i-table
+              - --i-mags
             argument: ARTIFACT
-            description: Feature table containing all features that should be used for target prediction. [required]
-          - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Numeric metadata column to use as prediction target.
-          - names:
-              - --p-cv
-            argument: INTEGER
-            description: Number of k-fold cross-validations to perform.
-          - names:
-              - --p-random-state
-            argument: INTEGER
-            description: Seed used by random number generator. [optional]
-          - names:
-              - --p-n-jobs
-            argument: NTHREADS
-            description: 'Number of jobs to run in parallel. [default: 1]'
+            description: MAGs to partition. [required]
           - names:
-              - --p-n-estimators
+              - --p-num-partitions
             argument: INTEGER
-            description: Number of trees to grow for estimation.
-          - names:
-              - --p-estimator
-            argument: '{RandomForestRegressor, ExtraTreesRegressor, GradientBoostingRegressor, AdaBoostRegressor, ElasticNet, Ridge, Lasso, KNeighborsRegressor, LinearSVR, SVR}'
-            description: Estimator method to use for sample prediction.
-          - names:
-              - --p-stratify
-              - --p-no-stratify
-            argument: ""
-            description: 'Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: False]'
-          - names:
-              - --p-parameter-tuning
-              - --p-no-parameter-tuning
-            argument: ""
-            description: 'Automatically tune hyperparameters using random grid search. [default: False]'
-          - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
-          - names:
-              - --o-predictions
-            argument: ARTIFACT SampleData[RegressorPredictions]
-            description: Predicted target values for each input sample. [required]
+            description: The number of partitions to split the MAGs into.
           - names:
-              - --o-feature-importance
-            argument: ARTIFACT FeatureData[Importance]
-            description: Importance of each input feature to model accuracy. [required]
+              - --o-partitioned-mags
+            argument: ARTIFACTS...
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -11407,26 +16227,21 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: scatterplot
-        description: Make 2D scatterplot and linear regression of
-        usage: qiime sample-classifier scatterplot [OPTIONS]
+      - name: partition-orthologs
+        description: Partition orthologs
+        usage: qiime moshpit partition-orthologs [OPTIONS]
         options:
           - names:
-              - --i-predictions
-            argument: ARTIFACT SampleData[RegressorPredictions]
-            description: Predicted values to plot on y axis. Must be predictions of numeric data produced by a sample regressor. [required]
-          - names:
-              - --m-truth-file
-              - --m-truth-column
-            argument: METADATA
-            description: Metadata column (true values) to plot on x axis.
+              - --i-orthologs
+            argument: ARTIFACT
+            description: The orthologs to partition. [required]
           - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
+              - --p-num-partitions
+            argument: INTEGER
+            description: The number of partitions to split the MAGs into.
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
+              - --o-partitioned-orthologs
+            argument: ARTIFACTS...
             description: '[required]'
           - names:
               - --output-dir
@@ -11449,52 +16264,22 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: split-table
-        description: Split a feature table into training and testing
-        usage: qiime sample-classifier split-table [OPTIONS]
+      - name: partition-sample-data-mags
+        description: Partition MAGs
+        usage: qiime moshpit partition-sample-data-mags [OPTIONS]
         options:
           - names:
-              - --i-table
+              - --i-mags
             argument: ARTIFACT
-            description: Feature table containing all features that should be used for target prediction.
-          - names:
-              - --m-metadata-file
-              - --m-metadata-column
-            argument: METADATA
-            description: Numeric metadata column to use as prediction target.
-          - names:
-              - --p-test-size
-            argument: PROPORTION
-            description: Fraction of input samples to exclude from training set and use for classifier testing.
+            description: The MAGs to partition. [required]
           - names:
-              - --p-random-state
+              - --p-num-partitions
             argument: INTEGER
-            description: Seed used by random number generator. [optional]
-          - names:
-              - --p-stratify
-              - --p-no-stratify
-            argument: ""
-            description: 'Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples. [default: True]'
-          - names:
-              - --p-missing-samples
-            argument: TEXT Choices('error', 'ignore')
-            description: 'How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. [default: ''error'']'
-          - names:
-              - --o-training-table
-            argument: ARTIFACT FeatureTable
-            description: Feature table containing training samples [required]
+            description: Range(1, None) The number of partitions to split the MAGs into.
           - names:
-              - --o-test-table
-            argument: ARTIFACT FeatureTable
-            description: Feature table containing test samples [required]
-          - names:
-              - --o-training-targets
-            argument: ARTIFACT SampleData[TrueTargets]
-            description: Series containing true target values of train samples
-          - names:
-              - --o-test-targets
-            argument: ARTIFACT SampleData[TrueTargets]
-            description: Series containing true target values of test samples
+              - --o-partitioned-mags
+            argument: ARTIFACTS...
+            description: '[required]'
           - names:
               - --output-dir
             argument: PATH
@@ -11516,18 +16301,30 @@ subcommands:
               - --help
             argument: ""
             description: Show this message and exit.
-      - name: summarize
-        description: Summarize parameter and feature extraction
-        usage: qiime sample-classifier summarize [OPTIONS]
+      - name: predict-genes-prodigal
+        description: Predict gene sequences from MAGs using Prodigal.
+        usage: qiime moshpit predict-genes-prodigal [OPTIONS]
         options:
           - names:
-              - --i-sample-estimator
-            argument: ""
-            description: ARTIFACT SampleEstimator[Classifier | Regressor] Sample estimator trained with fit_classifier or fit_regressor. [required]
+              - --i-mags
+            argument: ARTIFACT
+            description: MAGs for which one wishes to predict genes. [required]
           - names:
-              - --o-visualization
-            argument: VISUALIZATION
-            description: '[required]'
+              - --p-translation-table-number
+            argument: TEXT
+            description: Translation table to be used to translate genes into a sequence of amino acids..
+          - names:
+              - --o-loci
+            argument: ARTIFACT
+            description: Gene coordinates files (one per MAG) listing the location of each predicted gene as well as some additional scoring information. [required]
+          - names:
+              - --o-genes
+            argument: ARTIFACT
+            description: Fasta files (one per MAG) with the nucleotide sequences of the predicted genes. [required]
+          - names:
+              - --o-proteins
+            argument: ARTIFACT GenomeData[Proteins]
+            description: Fasta files (one per MAG) with the protein translation of the predicted genes. [required]
           - names:
               - --output-dir
             argument: PATH
diff --git a/bio/zsh b/bio/zsh
index 368bf100..06531ac7 160000
--- a/bio/zsh
+++ b/bio/zsh
@@ -1 +1 @@
-Subproject commit 368bf10006d9143ae4d60c824336e503bbb5ea88
+Subproject commit 06531ac73ce9b5883dda34fd7c3ead3ead476b85