Pharokka wrapper #5130
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| owner: iuc | ||
| name: pharokka | ||
| description: rapid standardised annotation tool for bacteriophage genomes and metagenomes | ||
| long_description: | | ||
| pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. | ||
| If you are looking for rapid standardised annotation of bacterial genomes, please use prokka, | ||
| which inspired the creation of pharokka, or bakta. Repository-Maintainer: Paul Zierep | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka | ||
| categories: | ||
| - Genome annotation | ||
| homepage_url: https://github.com/gbouras13/pharokka | ||
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| <?xml version="1.0"?> | ||
| <macros> | ||
| <token name="@TOOL_VERSION@">1.2.0</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">21.05</token> | ||
| <xml name="biotools"> | ||
| <xrefs> | ||
| <xref type="bio.tools"> | ||
| pharokka | ||
| </xref> | ||
| </xrefs> | ||
| </xml> | ||
| <xml name="requirements"> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@"> | ||
| pharokka | ||
| </requirement> | ||
| <requirement type="package" version="3.0"> | ||
| zip | ||
| </requirement> | ||
| </requirements> | ||
| </xml> | ||
| <xml name="version"> | ||
| <version_command> | ||
| pharokka.py --version | ||
| </version_command> | ||
| </xml> | ||
| <xml name="citations"> | ||
| <citations> | ||
| <citation type="doi"> | ||
| 10.1093/bioinformatics/btac776 | ||
| </citation> | ||
| </citations> | ||
| </xml> | ||
| </macros> |
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| <tool id="pharokka" name="bacteriophage annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.7" profile="@PROFILE@"> | ||
|
There was a problem hiding this comment. please remove the python_template_version its not needed. |
||
| <description> | ||
| rapid standardised annotation tool for bacteriophage genomes and metagenomes | ||
| </description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="biotools" /> | ||
| <expand macro="requirements" /> | ||
| <expand macro="version" /> | ||
| <command detect_errors="exit_code"> | ||
| <![CDATA[ | ||
| ## run tool | ||
| #if str( $terminase.terminase_selector ) == 'no_terminase': | ||
|
There was a problem hiding this comment. isn't there a else case missing for run_terminase? |
||
| pharokka.py | ||
| -i '$fasta' | ||
| -o pharokka_output | ||
| -d '$db_cached.fields.path' | ||
| -t \${GALAXY_SLOTS:-8} | ||
| $gene_predictor | ||
| $meta | ||
| -e '$evalue' && | ||
| #else: | ||
| pharokka.py | ||
| -i '$fasta' | ||
| -o pharokka_output | ||
| -d '$db_cached.fields.path' | ||
| -t \${GALAXY_SLOTS:-8} | ||
| $gene_predictor | ||
| $meta | ||
| -e '$evalue' | ||
| --terminase | ||
| --terminase_strand '$terminase.terminase_strand' | ||
| --terminase_start '$terminase.terminase_start' && | ||
| #end if | ||
|
|
||
| ## create output | ||
| #if $zip_output == 'true': | ||
| zip -r out.zip pharokka_output | ||
| #else: | ||
|
There was a problem hiding this comment. this else should not be needed |
||
| echo 'no zip output' | ||
| #end if | ||
| ]]> | ||
| </command> | ||
| <inputs> | ||
| <!-- the genome --> | ||
| <param type="data" name="fasta" format="fasta" help="Please upload an genome file of a bacteriophage in fasta format." label="Bacteriophage genome" /> | ||
| <param name="db_cached" type="select" label="Using built-in pharokka DB" help="Using built-in pharokka DB"> | ||
| <options from_data_table="pharokka_db"> | ||
| </options> | ||
| <validator type="no_options" message="A built-in pharokka DB is not available. Please ask the galaxy admins to install one on the server." /> | ||
| </param> | ||
| <param name="gene_predictor" type="select" label="User specified gene predictor"> | ||
| <option value="-g phanotate"> | ||
| Phanotate | ||
| </option> | ||
| <option value="-g prodigal"> | ||
| Prodigal | ||
| </option> | ||
| </param> | ||
| <param name="meta" type="boolean" checked="false" truevalue="--meta" falsevalue="" label="meta mode for metavirome input samples" /> | ||
| <param name="evalue" type="integer" value="100000" label="E-value threshold for mmseqs2 PHROGs database search. Defaults to 1E-05." /> | ||
|
There was a problem hiding this comment. please use min and max value whenever you can for floats and ints. the value looks for an evalue strange. There was a problem hiding this comment. I changed it, but the values go from 1e-20 to 10, however the bar does not really allow choosing something like 1e-10 ... I think it would be a good feature if a log scale could be used... There was a problem hiding this comment. But max 10 you can add correct? |
||
| <!-- optional arguments --> | ||
| <conditional name="terminase"> | ||
| <param name="terminase_selector" type="select" label="Runs - terminase large subunit - re-orientation mode. Single genome input only and requires --terminase_strand and --terminase_start to be specified."> | ||
| <option value="no_terminase"> | ||
| Do not run 'terminase large subunit' re-orientation mode. | ||
| </option> | ||
| <option value="run_terminase"> | ||
| Runs 'terminase large subunit' re-orientation mode. | ||
| </option> | ||
| </param> | ||
| <when value="no_terminase"> | ||
| </when> | ||
| <when value="run_terminase"> | ||
| <param name="terminase_strand" type="select" label="Strand of terminase large subunit."> | ||
| <option value="pos"> | ||
| Positive | ||
| </option> | ||
| <option value="neg"> | ||
| Negative | ||
| </option> | ||
| </param> | ||
| <param name="terminase_start" type="integer" value="1" label="Start coordinate of the terminase large subunit." /> | ||
| </when> | ||
| </conditional> | ||
| <!-- optional outputs --> | ||
| <param name="zip_output" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Create a Zip archive of the complete output for further investigation." /> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="pharokka_gbk" format="genbank" from_work_dir="pharokka_output/pharokka.gbk" label="${tool.name} on ${on_string}: Genbank" /> | ||
| <data name="pharokka_gff" format="gff" from_work_dir="pharokka_output/pharokka.gff" label="${tool.name} on ${on_string}: GFF" /> | ||
| <data name="archive_output" format="zip" from_work_dir="out.zip" label="${tool.name} on ${on_string}: zip of the complete output" > | ||
| <filter>zip_output</filter> | ||
| </data> | ||
|
|
||
| </outputs> | ||
| <tests> | ||
| <!-- test input from DB - no zip --> | ||
| <test expect_num_outputs="2"> | ||
| <param name="db_cached" value="pharokka_db" /> | ||
| <param name="fasta" value="SAOMS1.fasta" /> | ||
| <param name="zip_output" value="false" /> | ||
| <!-- check file size and text since output is non-deterministic --> | ||
| <output name="pharokka_gbk"> | ||
| <assert_contents> | ||
| <has_size value="353875" delta="10" /> | ||
| <has_text text="VERSION MW460250_1" /> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="pharokka_gff"> | ||
| <assert_contents> | ||
| <has_size value="191497" delta="10" /> | ||
| <has_text text="##sequence-region MW460250_1 1 140135" /> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <!-- test input from DB --> | ||
| <test expect_num_outputs="3"> | ||
| <param name="db_cached" value="pharokka_db" /> | ||
| <param name="fasta" value="SAOMS1.fasta" /> | ||
| <param name="zip_output" value="true" /> | ||
| <!-- check file size and text since output is non-deterministic --> | ||
| <output name="pharokka_gbk"> | ||
| <assert_contents> | ||
| <has_size value="353875" delta="10" /> | ||
| <has_text text="VERSION MW460250_1" /> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="pharokka_gff"> | ||
| <assert_contents> | ||
| <has_size value="191497" delta="10" /> | ||
| <has_text text="##sequence-region MW460250_1 1 140135" /> | ||
| </assert_contents> | ||
| </output> | ||
| <!-- check created zip --> | ||
| <output name="archive_output"> | ||
| <assert_contents> | ||
| <has_archive_member path=".*\/pharokka\.gff" /> | ||
| <has_archive_member path=".*\/pharokka\.gbk" /> | ||
| <has_archive_member path=".*\/pharokka.*\.log" /> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| <![CDATA[ | ||
| pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. | ||
|
|
||
| If you are looking for rapid standardised annotation of bacterial genomes, please use prokka, which inspired the creation of pharokka, or bakta. | ||
|
There was a problem hiding this comment. bakta should be used today, so I guess its save to recommend bakta. |
||
| ]]> | ||
| </help> | ||
| <expand macro="citations" /> | ||
| </tool> | ||
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You can get credits by adding tags to the tools ... see https://docs.galaxyproject.org/en/latest/dev/schema.html
And add yourself as maintainer via the codeowner file in this repo.