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+---
+site: freiburg
+tags: [tools]
+title: UseGalaxy.eu Tool Updates for 2024-03-17
+supporters:
+- denbi
+- elixir
+---
+
+On 2024-03-17, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #436](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#436/)
+
+
+## Graph/Display Data
+
+- pygenometracks was updated to [36b848d5f3ec](https://toolshed.g2.bx.psu.edu/view/iuc/pygenometracks/36b848d5f3ec)
+
+## GIS Data Handling
+
+- interpolation_run_idw_interpolation was updated to [b4b9edf9ea27](https://toolshed.g2.bx.psu.edu/view/ecology/interpolation_run_idw_interpolation/b4b9edf9ea27)
+- otb_band_math was updated to [0ed34e3202b9](https://toolshed.g2.bx.psu.edu/view/ecology/otb_band_math/0ed34e3202b9)
+- otb_mean_shift_smoothing was updated to [6c6e8b16dba6](https://toolshed.g2.bx.psu.edu/view/ecology/otb_mean_shift_smoothing/6c6e8b16dba6)
+
+## Metabolomics
+
+- assign_ri_from_comment was updated to [6975af39ba79](https://toolshed.g2.bx.psu.edu/view/recetox/assign_ri_from_comment/6975af39ba79)
+- matchms_add_key was updated to [a14e7fe18387](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_add_key/a14e7fe18387)
+- matchms_convert was updated to [165f303aa2d1](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_convert/165f303aa2d1)
+- matchms_convert was updated to [1f063ff015b9](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_convert/1f063ff015b9)
+- matchms_filtering was updated to [3370f5b08d19](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_filtering/3370f5b08d19)
+- matchms_fingerprint_similarity was updated to [1d3ee4f9f63d](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_fingerprint_similarity/1d3ee4f9f63d)
+- matchms_fingerprint_similarity was updated to [99da744050b7](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_fingerprint_similarity/99da744050b7)
+- matchms_formatter was updated to [23d4bc72c505](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_formatter/23d4bc72c505)
+- matchms_formatter was updated to [9287136a396a](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_formatter/9287136a396a)
+- matchms_metadata_export was updated to [786df5cf7dec](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_export/786df5cf7dec)
+- matchms_metadata_match was updated to [7d171a8c71dc](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_match/7d171a8c71dc)
+- matchms_metadata_merge was updated to [0c9f977e8d75](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_merge/0c9f977e8d75)
+- matchms_networking was updated to [2200e9b7a2b3](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_networking/2200e9b7a2b3)
+- matchms_networking was updated to [7985c63a880c](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_networking/7985c63a880c)
+- matchms_remove_key was updated to [8a8a58be3929](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_remove_key/8a8a58be3929)
+- matchms_spectral_similarity was updated to [44e7027714d7](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_spectral_similarity/44e7027714d7)
+- matchms_spectral_similarity was updated to [67f65bcc94bf](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_spectral_similarity/67f65bcc94bf)
+- matchms_split was updated to [114617e6ad33](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_split/114617e6ad33)
+- matchms_split was updated to [986ecfc55ed9](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_split/986ecfc55ed9)
+- matchms_subsetting was updated to [4ef214cf07c1](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_subsetting/4ef214cf07c1)
+- matchms_subsetting was updated to [9231f7bee46d](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_subsetting/9231f7bee46d)
+- use_theoretical_mz_annotations was updated to [e0cac9994a72](https://toolshed.g2.bx.psu.edu/view/recetox/use_theoretical_mz_annotations/e0cac9994a72)
+
+## ChemicalToolBox
+
+- qcxms_getres was updated to [ef51824f6d04](https://toolshed.g2.bx.psu.edu/view/recetox/qcxms_getres/ef51824f6d04)
+- qcxms_neutral_run was updated to [0d9d72ef658f](https://toolshed.g2.bx.psu.edu/view/recetox/qcxms_neutral_run/0d9d72ef658f)
+- qcxms_production_run was updated to [b566b27247f7](https://toolshed.g2.bx.psu.edu/view/recetox/qcxms_production_run/b566b27247f7)
+
+## QIIME 2
+
+- qiime2__deblur__denoise_16S was updated to [2572fc0f88f2](https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2)
+- qiime2__deblur__denoise_16S was updated to [b883cbea5623](https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623)
+
+## Get Data
+
+- unipept was updated to [21a560af5913](https://toolshed.g2.bx.psu.edu/view/galaxyp/unipept/21a560af5913)
+- sra_tools was updated to [1ec814014652](https://toolshed.g2.bx.psu.edu/view/iuc/sra_tools/1ec814014652)
+
+## Metagenomic Analysis
+
+- kraken was updated to [766d5f63b0f4](https://toolshed.g2.bx.psu.edu/view/devteam/kraken/766d5f63b0f4)
+- kraken_filter was updated to [67236d921e83](https://toolshed.g2.bx.psu.edu/view/devteam/kraken_filter/67236d921e83)
+- kraken_report was updated to [1c677354ab18](https://toolshed.g2.bx.psu.edu/view/devteam/kraken_report/1c677354ab18)
+- kraken_translate was updated to [8cebdc74a48f](https://toolshed.g2.bx.psu.edu/view/devteam/kraken_translate/8cebdc74a48f)
+- ampvis2_alpha_diversity was updated to [52fbe4eb7ce7](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_alpha_diversity/52fbe4eb7ce7)
+- ampvis2_boxplot was updated to [b4c6f8741989](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_boxplot/b4c6f8741989)
+- ampvis2_core was updated to [943c2ae9594a](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_core/943c2ae9594a)
+- ampvis2_export_fasta was updated to [c1fcdec30d69](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_export_fasta/c1fcdec30d69)
+- ampvis2_frequency was updated to [ac9564dcdb99](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_frequency/ac9564dcdb99)
+- ampvis2_heatmap was updated to [14695ae019be](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_heatmap/14695ae019be)
+- ampvis2_load was updated to [3481feabc54e](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_load/3481feabc54e)
+- ampvis2_merge_ampvis2 was updated to [d8334b328618](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_merge_ampvis2/d8334b328618)
+- ampvis2_mergereplicates was updated to [63ed7a3cd45f](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_mergereplicates/63ed7a3cd45f)
+- ampvis2_octave was updated to [4289db874e3c](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_octave/4289db874e3c)
+- ampvis2_ordinate was updated to [811df76f4f26](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_ordinate/811df76f4f26)
+- ampvis2_otu_network was updated to [7e6f33f40312](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_otu_network/7e6f33f40312)
+- ampvis2_rankabundance was updated to [d02f4a87eb55](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_rankabundance/d02f4a87eb55)
+- ampvis2_rarecurve was updated to [2e69edaaa834](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_rarecurve/2e69edaaa834)
+- ampvis2_setmetadata was updated to [b8fd62239d7e](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_setmetadata/b8fd62239d7e)
+- ampvis2_subset_samples was updated to [c8bfb923d7d4](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_subset_samples/c8bfb923d7d4)
+- ampvis2_subset_taxa was updated to [e2df49914652](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_subset_taxa/e2df49914652)
+- ampvis2_timeseries was updated to [9de032723f5b](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_timeseries/9de032723f5b)
+- ampvis2_venn was updated to [338f47a9e25c](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_venn/338f47a9e25c)
+- kraken_biom was updated to [b582a159bb10](https://toolshed.g2.bx.psu.edu/view/iuc/kraken_biom/b582a159bb10)
+- kraken_taxonomy_report was updated to [bfae8da6082c](https://toolshed.g2.bx.psu.edu/view/iuc/kraken_taxonomy_report/bfae8da6082c)
+- maaslin2 was updated to [ef2cace85809](https://toolshed.g2.bx.psu.edu/view/iuc/maaslin2/ef2cace85809)
+- mapseq was updated to [f1d1dafc836d](https://toolshed.g2.bx.psu.edu/view/iuc/mapseq/f1d1dafc836d)
+- nonpareil was updated to [cef64c36c89e](https://toolshed.g2.bx.psu.edu/view/iuc/nonpareil/cef64c36c89e)
+- phyloseq_from_dada2 was updated to [87064cb77a52](https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_dada2/87064cb77a52)
+- phyloseq_plot_ordination was updated to [dfe800a3faaf](https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_ordination/dfe800a3faaf)
+- phyloseq_plot_richness was updated to [fb7c4bbe8994](https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_richness/fb7c4bbe8994)
+- plasflow was updated to [1d2a91ab28b7](https://toolshed.g2.bx.psu.edu/view/iuc/plasflow/1d2a91ab28b7)
+- scoary was updated to [77d50ec2bcf2](https://toolshed.g2.bx.psu.edu/view/iuc/scoary/77d50ec2bcf2)
+- seqsero2 was updated to [5a9a6074d99b](https://toolshed.g2.bx.psu.edu/view/iuc/seqsero2/5a9a6074d99b)
+- vegan_diversity was updated to [a1b80a746054](https://toolshed.g2.bx.psu.edu/view/iuc/vegan_diversity/a1b80a746054)
+- vegan_fisher_alpha was updated to [0148e5cf20b2](https://toolshed.g2.bx.psu.edu/view/iuc/vegan_fisher_alpha/0148e5cf20b2)
+- vegan_rarefaction was updated to [af1211ed6c8e](https://toolshed.g2.bx.psu.edu/view/iuc/vegan_rarefaction/af1211ed6c8e)
+
+## FASTA/FASTQ
+
+- lighter was updated to [89b453176d05](https://toolshed.g2.bx.psu.edu/view/bgruening/lighter/89b453176d05)
+- ncbi_fcs_gx was updated to [3cdb96f2855d](https://toolshed.g2.bx.psu.edu/view/iuc/ncbi_fcs_gx/3cdb96f2855d)
+
+## Annotation
+
+- compleasm was updated to [79413aecc398](https://toolshed.g2.bx.psu.edu/view/iuc/compleasm/79413aecc398)
+- kofamscan was updated to [95c71179a054](https://toolshed.g2.bx.psu.edu/view/iuc/kofamscan/95c71179a054)
+- krocus was updated to [6a97c3a857d2](https://toolshed.g2.bx.psu.edu/view/iuc/krocus/6a97c3a857d2)
+- legsta was updated to [0411fca1d681](https://toolshed.g2.bx.psu.edu/view/iuc/legsta/0411fca1d681)
+- lorikeet_spoligotype was updated to [da22667725c7](https://toolshed.g2.bx.psu.edu/view/iuc/lorikeet_spoligotype/da22667725c7)
+- miniprot was updated to [00b22efdd100](https://toolshed.g2.bx.psu.edu/view/iuc/miniprot/00b22efdd100)
+- miniprot_index was updated to [9e2772125405](https://toolshed.g2.bx.psu.edu/view/iuc/miniprot_index/9e2772125405)
+- mirmachine was updated to [f2e87c81497d](https://toolshed.g2.bx.psu.edu/view/iuc/mirmachine/f2e87c81497d)
+- omark was updated to [9607b69326e1](https://toolshed.g2.bx.psu.edu/view/iuc/omark/9607b69326e1)
+- prodigal was updated to [91791b6ecd38](https://toolshed.g2.bx.psu.edu/view/iuc/prodigal/91791b6ecd38)
+- tbprofiler was updated to [d03af1c7002c](https://toolshed.g2.bx.psu.edu/view/iuc/tbprofiler/d03af1c7002c)
+- transtermhp was updated to [42b38f6d9f68](https://toolshed.g2.bx.psu.edu/view/iuc/transtermhp/42b38f6d9f68)
+- tsebra was updated to [f124679db9df](https://toolshed.g2.bx.psu.edu/view/iuc/tsebra/f124679db9df)
+
+## Proteomics
+
+- msstats was updated to [de7593c29499](https://toolshed.g2.bx.psu.edu/view/galaxyp/msstats/de7593c29499)
+- openms_openpepxl was updated to [40cc19c0dbd6](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/40cc19c0dbd6)
+- openms_openpepxl was updated to [a2a842b00f9c](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c)
+- openms_openpepxl was updated to [fc36cfd19834](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/fc36cfd19834)
+- openms_percolatoradapter was updated to [0fc9ae55bcfc](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc)
+- openms_percolatoradapter was updated to [e7881a82b56d](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d)
+- openms_xfdr was updated to [81402a5e4173](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173)
+- openms_xfdr was updated to [9a6e3bb0f358](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358)
+
+## Convert Formats
+
+- mz_to_sqlite was updated to [705821bf30d2](https://toolshed.g2.bx.psu.edu/view/galaxyp/mz_to_sqlite/705821bf30d2)
+- bam2fastx was updated to [61a6b93ee6e1](https://toolshed.g2.bx.psu.edu/view/iuc/bam2fastx/61a6b93ee6e1)
+- biom_convert was updated to [d4d4e9febf5c](https://toolshed.g2.bx.psu.edu/view/iuc/biom_convert/d4d4e9febf5c)
+
+## Machine Learning
+
+- biomodels_biomd0000001066 was updated to [1748c5d74df5](https://toolshed.g2.bx.psu.edu/view/bgruening/biomodels_biomd0000001066/1748c5d74df5)
+
+## Mapping
+
+- graphmap_align was updated to [1c6c961851de](https://toolshed.g2.bx.psu.edu/view/bgruening/graphmap_align/1c6c961851de)
+- graphmap_overlap was updated to [815251b32ccc](https://toolshed.g2.bx.psu.edu/view/bgruening/graphmap_overlap/815251b32ccc)
+
+## Imaging
+
+- points2binaryimage was updated to [2ad6350df85b](https://toolshed.g2.bx.psu.edu/view/imgteam/points2binaryimage/2ad6350df85b)
+
+## Assembly
+
+- miniasm was updated to [b799a615995d](https://toolshed.g2.bx.psu.edu/view/iuc/miniasm/b799a615995d)
+
+## Genome editing
+
+- crispr_studio was updated to [a227c05e0a55](https://toolshed.g2.bx.psu.edu/view/iuc/crispr_studio/a227c05e0a55)
+- sonneityping was updated to [0ac12c344bfa](https://toolshed.g2.bx.psu.edu/view/iuc/sonneityping/0ac12c344bfa)
+
+## Nanopore
+
+- nanopolishcomp_eventaligncollapse was updated to [74d7b06c2b92](https://toolshed.g2.bx.psu.edu/view/iuc/nanopolishcomp_eventaligncollapse/74d7b06c2b92)
+- nanopolishcomp_freqmethcalculate was updated to [f08dfdcefdbd](https://toolshed.g2.bx.psu.edu/view/iuc/nanopolishcomp_freqmethcalculate/f08dfdcefdbd)
+- pycoqc was updated to [3a2f2e24c37e](https://toolshed.g2.bx.psu.edu/view/iuc/pycoqc/3a2f2e24c37e)
+- pycoqc was updated to [fae03f3d4bf7](https://toolshed.g2.bx.psu.edu/view/iuc/pycoqc/fae03f3d4bf7)
+
+## Phylogenetics
+
+- hyphy_prime was updated to [4072360120e4](https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_prime/4072360120e4)
+- nextalign was updated to [aadc5d8099e2](https://toolshed.g2.bx.psu.edu/view/iuc/nextalign/aadc5d8099e2)
+- nextclade was updated to [4f6349228462](https://toolshed.g2.bx.psu.edu/view/iuc/nextclade/4f6349228462)
+
+## SAM/BAM
+
+- bamtools was updated to [970e6333f07e](https://toolshed.g2.bx.psu.edu/view/devteam/bamtools/970e6333f07e)
+- bamtools_filter was updated to [993b19f20c76](https://toolshed.g2.bx.psu.edu/view/devteam/bamtools_filter/993b19f20c76)
+- bamtools_split_mapped was updated to [fa7b5520ae53](https://toolshed.g2.bx.psu.edu/view/iuc/bamtools_split_mapped/fa7b5520ae53)
+- bamtools_split_paired was updated to [75d5afa09972](https://toolshed.g2.bx.psu.edu/view/iuc/bamtools_split_paired/75d5afa09972)
+- bamtools_split_ref was updated to [9b8feb118f9e](https://toolshed.g2.bx.psu.edu/view/iuc/bamtools_split_ref/9b8feb118f9e)
+- bamtools_split_tag was updated to [e9b9c489aacc](https://toolshed.g2.bx.psu.edu/view/iuc/bamtools_split_tag/e9b9c489aacc)
+
+## Single-cell
+
+- scanpy_cluster_reduce_dimension was updated to [6f83f8fd381f](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_cluster_reduce_dimension/6f83f8fd381f)
+- scanpy_filter was updated to [277313130da5](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_filter/277313130da5)
+- scanpy_inspect was updated to [5c3ebe2adc77](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_inspect/5c3ebe2adc77)
+- scanpy_normalize was updated to [7b9fafe32c86](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_normalize/7b9fafe32c86)
+- scanpy_plot was updated to [6f5349dd5c49](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_plot/6f5349dd5c49)
+- scanpy_remove_confounders was updated to [d18e7a6e5cd4](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_remove_confounders/d18e7a6e5cd4)
+
+## Variant Calling
+
+- cnv_phenopacket was updated to [61aad58c7b2d](https://toolshed.g2.bx.psu.edu/view/iuc/cnv_phenopacket/61aad58c7b2d)
+- cnv_vcf2json was updated to [c8caf812d33b](https://toolshed.g2.bx.psu.edu/view/iuc/cnv_vcf2json/c8caf812d33b)
+
+## Virology
+
+- ivar_consensus was updated to [40737febe339](https://toolshed.g2.bx.psu.edu/view/iuc/ivar_consensus/40737febe339)
+- ivar_filtervariants was updated to [096a5b0210cc](https://toolshed.g2.bx.psu.edu/view/iuc/ivar_filtervariants/096a5b0210cc)
+- ivar_filtervariants was updated to [618297d23022](https://toolshed.g2.bx.psu.edu/view/iuc/ivar_filtervariants/618297d23022)
+- ivar_removereads was updated to [a1c2aecd7a0d](https://toolshed.g2.bx.psu.edu/view/iuc/ivar_removereads/a1c2aecd7a0d)
+- ivar_trim was updated to [28e4bcbc86e7](https://toolshed.g2.bx.psu.edu/view/iuc/ivar_trim/28e4bcbc86e7)
+- ivar_trim was updated to [86a20ae274fc](https://toolshed.g2.bx.psu.edu/view/iuc/ivar_trim/86a20ae274fc)
+- ivar_variants was updated to [194e3ceee923](https://toolshed.g2.bx.psu.edu/view/iuc/ivar_variants/194e3ceee923)
+- read_it_and_keep was updated to [fa7086274673](https://toolshed.g2.bx.psu.edu/view/iuc/read_it_and_keep/fa7086274673)
+
+## None
+
+- data_manager_diamond_database_builder was updated to [4a08b7b76b78](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78)
+
+## hca_sc_label_analysis_tools
+
+- decoupler_pseudobulk was updated to [130e25d3ce92](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/decoupler_pseudobulk/130e25d3ce92)
+- decoupler_pseudobulk was updated to [893ff9213a34](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/decoupler_pseudobulk/893ff9213a34)
+