From 82efc4990693ac74b6a657aa464e2334b80406ed Mon Sep 17 00:00:00 2001 From: github-actions Date: Sun, 9 Jun 2024 09:15:56 +0000 Subject: [PATCH] fetch all tools bot - step fetch --- results/repositories01.list_tools.json | 5842 ++++++++++++++++++++++-- results/repositories01.list_tools.tsv | 280 +- 2 files changed, 5702 insertions(+), 420 deletions(-) diff --git a/results/repositories01.list_tools.json b/results/repositories01.list_tools.json index 6913d40b..95e464f2 100644 --- a/results/repositories01.list_tools.json +++ b/results/repositories01.list_tools.json @@ -26,10 +26,48 @@ "Conda version": "3.58.1", "EDAM operation (no superclasses)": [], "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org (Main)": 0, "Available on UseGalaxy.org.au": 0, "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 0, + "Tools available on UseGalaxy.fr": 0, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 0, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CorGAT": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 0, + "Tools available on UseGalaxy.cz": 0, + "Tools available on UseGalaxy.no": 0 }, { "Galaxy wrapper id": "baric_archive", @@ -59,10 +97,48 @@ "Conda version": null, "EDAM operation (no superclasses)": [], "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org (Main)": 0, "Available on UseGalaxy.org.au": 0, "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 2 + "Available on UseGalaxy.fr": 2, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 0, + "Tools available on UseGalaxy.fr": 2, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 0, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CorGAT": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 0, + "Tools available on UseGalaxy.cz": 0, + "Tools available on UseGalaxy.no": 0 }, { "Galaxy wrapper id": "braker", @@ -91,10 +167,48 @@ "Conda version": null, "EDAM operation (no superclasses)": [], "EDAM topic (no superclasses)": [], - 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"Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org (Main)": 0, "Available on UseGalaxy.org.au": 0, "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 0, + "Tools available on UseGalaxy.fr": 0, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 0, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CorGAT": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 0, + "Tools available on UseGalaxy.cz": 0, + "Tools available on UseGalaxy.no": 0 }, { "Galaxy wrapper id": "suite_qiime2__sample_classifier", @@ -4691,10 +9783,48 @@ "Conda version": null, "EDAM operation (no superclasses)": [], "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 15, + "Available on UseGalaxy.org (Main)": 15, "Available on UseGalaxy.org.au": 15, "Available on UseGalaxy.eu": 15, - "Available on UseGalaxy.org.fr": 15 + "Available on UseGalaxy.fr": 15, + "Tools available on UseGalaxy.org (Main)": 15, + "Tools available on UseGalaxy.org.au": 15, + "Tools available on UseGalaxy.eu": 15, + "Tools available on UseGalaxy.fr": 15, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 0, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CorGAT": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 0, + "Tools available on UseGalaxy.cz": 15, + "Tools available on UseGalaxy.no": 0 }, { "Galaxy wrapper id": "suite_qiime2__taxa", @@ -4728,10 +9858,48 @@ "Conda version": null, "EDAM operation (no superclasses)": [], "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org (Main)": 4, "Available on UseGalaxy.org.au": 4, "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 4 + "Available on UseGalaxy.fr": 4, + "Tools available on UseGalaxy.org (Main)": 4, + "Tools available on UseGalaxy.org.au": 4, + "Tools available on UseGalaxy.eu": 4, + "Tools available on UseGalaxy.fr": 4, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 0, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CorGAT": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 0, + "Tools available on UseGalaxy.cz": 4, + "Tools available on UseGalaxy.no": 0 }, { "Galaxy wrapper id": "suite_qiime2__vsearch", @@ -4769,10 +9937,48 @@ "Conda version": null, "EDAM operation (no superclasses)": [], "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 8, + "Available on UseGalaxy.org (Main)": 8, "Available on UseGalaxy.org.au": 8, "Available on UseGalaxy.eu": 8, - "Available on UseGalaxy.org.fr": 7 + "Available on UseGalaxy.fr": 7, + "Tools available on UseGalaxy.org (Main)": 8, + "Tools available on UseGalaxy.org.au": 8, + "Tools available on UseGalaxy.eu": 8, + "Tools available on UseGalaxy.fr": 7, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 0, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CorGAT": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 0, + "Tools available on UseGalaxy.cz": 8, + "Tools available on UseGalaxy.no": 0 }, { "Galaxy wrapper id": "suite_qiime2_core__tools", @@ -4805,10 +10011,48 @@ "Conda version": null, "EDAM operation (no superclasses)": [], "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org (Main)": 2, "Available on UseGalaxy.org.au": 2, "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 + "Available on UseGalaxy.fr": 2, + "Tools available on UseGalaxy.org (Main)": 2, + "Tools available on UseGalaxy.org.au": 2, + "Tools available on UseGalaxy.eu": 2, + "Tools available on UseGalaxy.fr": 2, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 0, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CorGAT": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 0, + "Tools available on UseGalaxy.cz": 2, + "Tools available on UseGalaxy.no": 0 }, { "Galaxy wrapper id": "suite_qiime2_core", @@ -4837,9 +10081,47 @@ "Conda version": null, "EDAM operation (no superclasses)": [], "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org (Main)": 0, "Available on UseGalaxy.org.au": 0, "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 0, + "Tools available on UseGalaxy.fr": 0, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 0, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CorGAT": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 0, + "Tools available on UseGalaxy.cz": 0, + "Tools available on UseGalaxy.no": 0 } ] \ No newline at end of file diff --git a/results/repositories01.list_tools.tsv b/results/repositories01.list_tools.tsv index cb1edc53..15a0d97b 100644 --- a/results/repositories01.list_tools.tsv +++ b/results/repositories01.list_tools.tsv @@ -1,140 +1,140 @@ -Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.org.fr -Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests 0 0 3 0 -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 0 0 1 0 -TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics 0 0 1 0 -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 -apoc 3.0 1.0 apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 1 0 1 0 -apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 0 0 9 0 -askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 0 0 0 0 -askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 0 0 0 0 -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 -bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 0 0 0 0 -baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 0 0 0 2 -batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers batched_lastz richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1.04.22 lastz 1.04.22 1 0 0 0 -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 0 0 0 0 -biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter 0.2.0 pandas 0 0 0 0 -blast_parser 296.0 27.0 blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 0 0 1 0 -braker 109.0 17.0 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 0 0 1 0 -braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis 0 1 1 1 -bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.54 0 1 0 1 -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 1 2 2 2 -chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 0 0 0 0 -collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk 1 1 1 1 -combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 0 0 0 0 -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.54 0 0 0 0 -combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 0 0 0 0 -concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0.2 0 0 0 0 -correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 0 0 0 1 -cryptogenotyper 8518.0 16.0 CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 0 0 1 0 -csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0.20.0 csvtk 0.30.0 0 0 0 1 -ectyper 9907.0 53.0 ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 0 0 1 0 -ete 1255.0 67.0 ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 Phylogenetic tree editing Phylogenetics 0 0 7 7 -export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0.0.2 EXPORT_DIR_PREFIX 0 0 0 0 -fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 0 0 0 0 -fasta_extract 10.0 fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 0 0 0 0 -fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 0 0 0 0 -feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 0 0 0 0 -feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 0 0 0 0 -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b 0 1 0 1 -gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 0 0 0 0 -gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk 0 0 0 0 -genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io Up-to-date https://genenotebook.github.io Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.15 genoboo 0.4.15 0 0 1 1 -genform 68.0 genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 0 0 1 0 -get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python 0 0 0 0 -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 0 0 0 0 -gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 1.1.0 gnali 1.1.0 0 0 0 0 -gstf_preparation 397.0 4.0 gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python 0 0 1 0 -hcluster_sg 238.0 13.0 hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 0 0 1 0 -hcluster_sg_parser 290.0 7.0 hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 0 0 1 0 -helixer 93.0 1.0 helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 Gene prediction, Genome annotation Sequence analysis, Gene transcripts 0 0 1 1 -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 0 0 0 0 -influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.2 0 0 0 1 -influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.0.4 0 0 0 1 -ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 0 0 0 0 -isoplot 2.0 1.0 isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 0 0 1 1 -jbrowse 18229.0 2346.0 jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python 0 0 0 0 -kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b1 0 0 0 0 -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 0 0 0 0 -kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 2.3 kat 2.4.2 0 0 0 0 -kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python 0 0 0 0 -logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 0 0 0 0 -lotus2 936.0 114.0 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.32 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology 0 0 1 0 -mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 0 0 0 0 -meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 0 0 0 0 -miranda 6076.0 41.0 miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a 0 0 1 1 -miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl 0 0 0 0 -mixmodel4repeated_measures 47.0 2.0 mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 0 0 0 1 -mob_suite 89021.0 322.0 mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 0 2 2 2 -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 0 0 0 0 -ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base 0 0 0 1 -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base 0 0 0 0 -ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 1 0 0 0 -nmr_annotation 47.0 3.0 NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 0 0 1 1 -nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 0 0 0 1 -nmr_preprocessing 140.0 4.0 NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 0 2 2 2 -normalization 133.0 13.0 normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 0 1 1 1 -openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk 0 0 0 0 -pangolin 7276.0 259.0 pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 1 1 1 1 -patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python 0 0 0 0 -peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.0 0 0 0 0 -physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes To update physiofit.readthedocs.io Metabolomics physiofit workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.3.5 physiofit 3.3.6 0 0 0 1 -physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager Metabolomics physiofit_manager workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager 1.0.1 0 0 0 1 -plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0.1.6 r 0 0 0 0 -plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 0 0 0 0 -pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 1.2.1 pneumocat 1.2.1 0 0 0 0 -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 -pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 0 0 0 0 -quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 0 12 0 12 -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 0 0 0 0 -refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 0 0 0 2 -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 -replace_chromosome_names 537.0 20.0 replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0.1 python 0 0 1 0 -rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 0 0 0 0 -segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. To update https://github.com/gsneha26/SegAlign Next Gen Mappers segalign richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 0.1.2.2 segalign-full 0.1.2.3 1 0 0 0 -seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 0 0 0 0 -sistr_cmd 2489.0 133.0 sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 0 1 1 0 -skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 0 0 0 1 -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 0 0 0 0 -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 0 0 0 0 -smina 493.0 9.0 smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 1 0 1 0 -spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed 0 0 0 0 -spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 0 0 0 0 -spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred 0 0 0 0 -srst2 205.0 22.0 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 0 0 1 0 -staramr 12673.0 889.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 1 1 1 1 -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 0 0 0 0 -suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 -suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 -suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 -suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 -suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 -suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 -suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 21 21 -suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 -suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 -suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 10 10 10 10 -suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 17 17 17 17 -suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 -suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.5.0+q2galaxy.2024.5.0 11 11 11 11 -suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 -suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 -suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 -suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 -suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 -suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 -suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 -suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 -suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 -suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 -t_coffee 8690.0 70.0 t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b 0 0 1 0 -tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 1.1.0 perl-bioperl 1.7.8 0 0 0 0 -tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal python-tripal 3.2.1 0 0 0 0 -w4mclassfilter 2834.0 3.0 w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base 0 1 1 0 -w4mcorcov 368.0 5.0 w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base 0 1 1 0 -w4mjoinpn 171.0 2.0 w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 0 1 1 0 -wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 0 0 0 0 -xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram To update https://github.com/sneumann/xcms Metabolomics xcms workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms 3.12.0 bioconductor-xcms 4.0.0 9 9 10 10 +Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on ANASTASIA Tools available on APOSTL Tools available on ARGs-OAP Tools available on BF2I-MAP Tools available on BioBix Tools available on CIRM-CFBP Tools available on Center for Phage Technology (CPT) Tools available on ChemFlow Tools available on Coloc-stats Tools available on CorGAT Tools available on CropGalaxy Tools available on Dintor Tools available on FreeBioinfo Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on Protologger Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no +Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 +GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +apoc 3.0 1.0 apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 0 0 9 0 0 0 9 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 +askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers batched_lastz richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1.04.22 lastz 1.04.22 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter 0.2.0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +blast_parser 296.0 27.0 blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +braker 109.0 17.0 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 +braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 +bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.54 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 +camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 +chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 1 1 +combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +cryptogenotyper 8518.0 16.0 CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0.20.0 csvtk 0.30.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ectyper 9907.0 53.0 ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 +ete 1255.0 67.0 ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 Phylogenetic tree editing Phylogenetics 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 +export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0.0.2 EXPORT_DIR_PREFIX 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +fasta_extract 10.0 fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 +fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b 0 1 0 1 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io Up-to-date https://genenotebook.github.io Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.15 genoboo 0.4.15 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +genform 68.0 genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 1.1.0 gnali 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +gstf_preparation 397.0 4.0 gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +hcluster_sg 238.0 13.0 hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +hcluster_sg_parser 290.0 7.0 hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +helixer 93.0 1.0 helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 Gene prediction, Genome annotation Sequence analysis, Gene transcripts 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 +hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.2 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.0.4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +isoplot 2.0 1.0 isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 +jbrowse 18229.0 2346.0 jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +lotus2 936.0 114.0 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.32 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 +mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +miranda 6076.0 41.0 miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mixmodel4repeated_measures 47.0 2.0 mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mob_suite 89021.0 322.0 mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +nmr_annotation 47.0 3.0 NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +nmr_preprocessing 140.0 4.0 NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 +normalization 133.0 13.0 normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +pangolin 7276.0 259.0 pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 1 0 +patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes To update physiofit.readthedocs.io Metabolomics physiofit workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.3.5 physiofit 3.3.6 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager Metabolomics physiofit_manager workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager 1.0.1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0.1.6 r 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 +pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 1.2.1 pneumocat 1.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 0 12 0 12 0 12 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +replace_chromosome_names 537.0 20.0 replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. To update https://github.com/gsneha26/SegAlign Next Gen Mappers segalign richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 0.1.2.2 segalign-full 0.1.2.6 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +sistr_cmd 2489.0 133.0 sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +smina 493.0 9.0 smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +srst2 205.0 22.0 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 +staramr 12673.0 889.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 +stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 21 21 21 21 21 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 +suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 +suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 +suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 17 17 17 17 17 17 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.5.0+q2galaxy.2024.5.0 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +t_coffee 8690.0 70.0 t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b 0 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal python-tripal 3.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +w4mclassfilter 2834.0 3.0 w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +w4mcorcov 368.0 5.0 w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +w4mjoinpn 171.0 2.0 w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 +wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram To update https://github.com/sneumann/xcms Metabolomics xcms workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms 3.12.0 bioconductor-xcms 4.0.0 9 9 10 10 9 9 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 10 9